The goal of this analysis is to identify conserved versus human-specific tDMRs
# Import libraries
library("ggplot2")## Warning: package 'ggplot2' was built under R version 3.4.4library("VennDiagram")## Warning: package 'VennDiagram' was built under R version 3.4.4## Loading required package: grid## Loading required package: futile.loggerlibrary("plyr")
library("dplyr")## Warning: package 'dplyr' was built under R version 3.4.4##
## Attaching package: 'dplyr'## The following objects are masked from 'package:plyr':
##
## arrange, count, desc, failwith, id, mutate, rename, summarise,
## summarize## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, unionlibrary("bedr")##
##
## ######################
## #### bedr v1.0.4 ####
## ######################
##
## checking binary availability...
## * Checking path for bedtools... PASS
## /usr/local/bin/bedtools
## * Checking path for bedops... FAIL
## * Checking path for tabix... FAIL
## tests and examples will be skipped on R CMD check if binaries are missinglibrary("RColorBrewer")
getwd()## [1] "/Users/laurenblake/Desktop/Regulatory_Evol/ashlar-trial/analysis"colors <- colorRampPalette(c(brewer.pal(9, "Blues")[1],brewer.pal(9, "Blues")[9]))(100)
pal <- c(brewer.pal(9, "Set1"), brewer.pal(8, "Set2"), brewer.pal(12, "Set3"))
# Import the data
# Human tDMRs
humans_heart_kidney_DMRs <- read.delim("../data/humans_heart_kidney_DMRs.txt")
humans_heart_liver_DMRs <- read.delim("../data/humans_heart_liver_DMRs.txt")
humans_heart_lung_DMRs <- read.delim("../data/humans_heart_lung_DMRs.txt")
humans_liver_lung_DMRs <- read.delim("../data/humans_liver_lung_DMRs.txt")
humans_liver_kidney_DMRs <- read.delim("../data/humans_liver_kidney_DMRs.txt")
humans_lung_kidney_DMRs <- read.delim("../data/humans_lung_kidney_DMRs.txt")
levels(humans_lung_kidney_DMRs[,1])## [1] "chr1" "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16"
## [9] "chr17" "chr18" "chr19" "chr2" "chr20" "chr21" "chr22" "chr3"
## [17] "chr4" "chr5" "chr6" "chr7" "chr8" "chr9" "chrX"#count(humans_lung_kidney_DMRs[,1])
# Chimp tDMRs
chimps_heart_kidney_DMRs <- read.delim("../data/chimps_heart_kidney_DMRs.txt")
chimps_heart_liver_DMRs <- read.delim("../data/chimps_heart_liver_DMRs.txt")
chimps_heart_lung_DMRs <- read.delim("../data/chimps_heart_lung_DMRs.txt")
chimps_liver_lung_DMRs <- read.delim("../data/chimps_liver_lung_DMRs.txt")
chimps_liver_kidney_DMRs <- read.delim("../data/chimps_liver_kidney_DMRs.txt")
chimps_lung_kidney_DMRs <- read.delim("../data/chimps_lung_kidney_DMRs.txt")
levels(chimps_lung_kidney_DMRs[,1])## [1] "chr1" "chr10"
## [3] "chr11" "chr11_gl000202_random"
## [5] "chr12" "chr13"
## [7] "chr14" "chr15"
## [9] "chr16" "chr17"
## [11] "chr18" "chr19"
## [13] "chr2" "chr20"
## [15] "chr21" "chr22"
## [17] "chr3" "chr4"
## [19] "chr5" "chr6"
## [21] "chr7" "chr8"
## [23] "chr9" "chrX"#count(chimps_lung_kidney_DMRs[,1])
# Rhesus tDMRs
rhesus_heart_kidney_DMRs <- read.delim("../data/rhesus_heart_kidney_DMRs.txt")
rhesus_heart_liver_DMRs <- read.delim("../data/rhesus_heart_liver_DMRs.txt")
rhesus_heart_lung_DMRs <- read.delim("../data/rhesus_heart_lung_DMRs.txt")
rhesus_liver_lung_DMRs <- read.delim("../data/rhesus_liver_lung_DMRs.txt")
rhesus_liver_kidney_DMRs <- read.delim("../data/rhesus_liver_kidney_DMRs.txt")
rhesus_lung_kidney_DMRs <- read.delim("../data/rhesus_lung_kidney_DMRs.txt")
levels(rhesus_heart_kidney_DMRs[,1])## [1] "chr1" "chr10"
## [3] "chr11" "chr11_gl000202_random"
## [5] "chr12" "chr13"
## [7] "chr14" "chr15"
## [9] "chr16" "chr17"
## [11] "chr17_gl000204_random" "chr18"
## [13] "chr19" "chr2"
## [15] "chr20" "chr21"
## [17] "chr22" "chr3"
## [19] "chr4" "chr5"
## [21] "chr6" "chr7"
## [23] "chr8" "chr9"
## [25] "chrX"#count(rhesus_lung_kidney_DMRs[,1])# Human heart-liver
# columns to pull
pull_col <- c(1:3, 16)
# make bed style format
humans_heart_liver_DMRs_bed <- humans_heart_liver_DMRs[,pull_col]
# Get DMRs on the autosomal chromosomes only
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed[which(humans_heart_liver_DMRs_bed[,1] != "chrX"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
summary(humans_heart_liver_DMRs_bed_noX[,3] - humans_heart_liver_DMRs_bed_noX[,2])## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 5.0 255.0 473.0 584.5 795.0 4797.0humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr11_gl000202_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr17_gl000204_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
sort_humans_heart_liver_DMRs_bed <- bedr.sort.region(humans_heart_liver_DMRs_bed_noX)## SORTING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Overlapping regions can cause unexpected results.# Human heart-lung
# columns to pull
pull_col <- c(1:3, 16)
# make bed style format
humans_heart_liver_DMRs_bed <- humans_heart_lung_DMRs[,pull_col]
# Get DMRs on the autosomal chromosomes only
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed[which(humans_heart_liver_DMRs_bed[,1] != "chrX"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr11_gl000202_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr17_gl000204_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
sort_humans_heart_lung_DMRs_bed <- bedr.sort.region(humans_heart_liver_DMRs_bed_noX)## SORTING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Overlapping regions can cause unexpected results.# human heart-kidney
# columns to pull
pull_col <- c(1:3, 16)
# make bed style format
humans_heart_liver_DMRs_bed <- humans_heart_kidney_DMRs[,pull_col]
# Get DMRs on the autosomal chromosomes only
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed[which(humans_heart_liver_DMRs_bed[,1] != "chrX"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr11_gl000202_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr17_gl000204_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
summary(humans_heart_liver_DMRs_bed_noX[,3] - humans_heart_liver_DMRs_bed_noX[,2])## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 6.0 261.0 486.0 594.7 831.0 4630.0sort_humans_heart_kidney_DMRs_bed <- bedr.sort.region(humans_heart_liver_DMRs_bed_noX, check.chr = FALSE)## SORTING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Overlapping regions can cause unexpected results.# human liver-lung
# columns to pull
pull_col <- c(1:3, 16)
# make bed style format
humans_heart_liver_DMRs_bed <- humans_liver_lung_DMRs[,pull_col]
# Get DMRs on the autosomal chromosomes only
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed[which(humans_heart_liver_DMRs_bed[,1] != "chrX"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
summary(humans_heart_liver_DMRs_bed_noX[,3] - humans_heart_liver_DMRs_bed_noX[,2])## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 5.0 228.0 427.0 540.7 738.0 4768.0humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr11_gl000202_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr17_gl000204_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
sort_humans_liver_lung_DMRs_bed <- bedr.sort.region(humans_heart_liver_DMRs_bed_noX)## SORTING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Overlapping regions can cause unexpected results.# human liver-kidney
# columns to pull
pull_col <- c(1:3, 16)
# make bed style format
humans_heart_liver_DMRs_bed <- humans_liver_kidney_DMRs[,pull_col]
# Get DMRs on the autosomal chromosomes only
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed[which(humans_heart_liver_DMRs_bed[,1] != "chrX"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
summary(humans_heart_liver_DMRs_bed_noX[,3] - humans_heart_liver_DMRs_bed_noX[,2])## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 4 242 449 553 759 4245humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr11_gl000202_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr17_gl000204_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
sort_humans_liver_kidney_DMRs_bed <- bedr.sort.region(humans_heart_liver_DMRs_bed_noX)## SORTING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Overlapping regions can cause unexpected results.# human lung-kidney
# columns to pull
pull_col <- c(1:3, 16)
# make bed style format
humans_heart_liver_DMRs_bed <- humans_lung_kidney_DMRs[,pull_col]
# Get DMRs on the autosomal chromosomes only
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed[which(humans_heart_liver_DMRs_bed[,1] != "chrX"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr11_gl000202_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr17_gl000204_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
summary(humans_heart_liver_DMRs_bed_noX[,3] - humans_heart_liver_DMRs_bed_noX[,2])## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 5.0 241.0 445.0 544.4 757.0 3732.0sort_humans_lung_kidney_DMRs_bed <- bedr.sort.region(humans_heart_liver_DMRs_bed_noX)## SORTING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Overlapping regions can cause unexpected results.# 25% overlap
heart_liver_heart_lung_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_heart_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315541e7b4.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316ea21cb5.bed -wao -f 0.25 -F 0.25heart_liver_heart_kidney_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_heart_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316baf481f.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31b8ff262.bed -wao -f 0.25 -F 0.25heart_liver_liver_lung_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_liver_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3110a8da45.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315b0ec18.bed -wao -f 0.25 -F 0.25heart_liver_liver_kidney_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_liver_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317b0d1c0a.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b314513e46a.bed -wao -f 0.25 -F 0.25heart_liver_lung_kidney_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_lung_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31274be0e2.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3169a8c3c7.bed -wao -f 0.25 -F 0.25colnames(heart_liver_heart_lung_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_heart_kidney_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_liver_kidney_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_liver_lung_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_lung_kidney_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
head(heart_liver_heart_lung_only_75)## chr start end direction chr.b start.b end.b
## chr1:715109-715282 chr1 715109 715282 hyper . -1 -1
## chr1:766879-767252 chr1 766879 767252 hypo chr1 766672 767252
## chr1:800313-801775 chr1 800313 801775 hypo . -1 -1
## chr1:871334-871812 chr1 871334 871812 hypo chr1 871135 871870
## chr1:896748-896792 chr1 896748 896792 hypo . -1 -1
## chr1:908583-909092 chr1 908583 909092 hypo . -1 -1
## direction.b overlap
## chr1:715109-715282 . 0
## chr1:766879-767252 hypo 373
## chr1:800313-801775 . 0
## chr1:871334-871812 hypo 478
## chr1:896748-896792 . 0
## chr1:908583-909092 . 0head(heart_liver_heart_kidney_only_75)## chr start end direction chr.b start.b end.b direction.b overlap
## 1 chr1 715109 715282 hyper . -1 -1 . 0
## 2 chr1 766879 767252 hypo chr1 766672 767180 hypo 301
## 3 chr1 800313 801775 hypo chr1 800829 801915 hypo 946
## 4 chr1 871334 871812 hypo chr1 871301 871870 hypo 478
## 5 chr1 896748 896792 hypo . -1 -1 . 0
## 6 chr1 908583 909092 hypo . -1 -1 . 0head(heart_liver_liver_kidney_only_75)## chr start end direction chr.b start.b end.b direction.b overlap
## 1 chr1 715109 715282 hyper chr1 715109 715282 hypo 173
## 2 chr1 766879 767252 hypo . -1 -1 . 0
## 3 chr1 800313 801775 hypo . -1 -1 . 0
## 4 chr1 871334 871812 hypo . -1 -1 . 0
## 5 chr1 896748 896792 hypo . -1 -1 . 0
## 6 chr1 908583 909092 hypo . -1 -1 . 0head(heart_liver_liver_lung_only_75)## chr start end direction chr.b start.b end.b direction.b overlap
## 1 chr1 715109 715282 hyper chr1 715109 715282 hypo 173
## 2 chr1 766879 767252 hypo . -1 -1 . 0
## 3 chr1 800313 801775 hypo . -1 -1 . 0
## 4 chr1 871334 871812 hypo . -1 -1 . 0
## 5 chr1 896748 896792 hypo . -1 -1 . 0
## 6 chr1 908583 909092 hypo . -1 -1 . 0head(heart_liver_lung_kidney_only_75)## chr start end direction chr.b start.b end.b direction.b overlap
## 1 chr1 715109 715282 hyper . -1 -1 . 0
## 2 chr1 766879 767252 hypo . -1 -1 . 0
## 3 chr1 800313 801775 hypo . -1 -1 . 0
## 4 chr1 871334 871812 hypo . -1 -1 . 0
## 5 chr1 896748 896792 hypo . -1 -1 . 0
## 6 chr1 908583 909092 hypo . -1 -1 . 0human_heart_liver_DMR <- left_join(heart_liver_heart_lung_only_75, heart_liver_heart_kidney_only_75, by= c("chr", "start")) %>% left_join(., heart_liver_liver_lung_only_75, by=c("chr", "start")) %>% left_join(., heart_liver_liver_kidney_only_75, by=c("chr", "start")) %>% left_join(., heart_liver_lung_kidney_only_75, by=c("chr", "start"))
human_DMR_heart_specific_25 <- human_heart_liver_DMR[which(human_heart_liver_DMR[,9] > 0 & human_heart_liver_DMR[,16] > 0 & human_heart_liver_DMR[,23] < 1 & human_heart_liver_DMR[,30] < 1 & human_heart_liver_DMR[,37] < 1),]
dim(human_DMR_heart_specific_25)## [1] 2949 37# Same direction
human_DMR_heart_specific_25 <- human_DMR_heart_specific_25[which(human_DMR_heart_specific_25[,4] == human_DMR_heart_specific_25[,8]),]
human_DMR_heart_specific_25 <- human_DMR_heart_specific_25[which(human_DMR_heart_specific_25[,4] == human_DMR_heart_specific_25[,11]),]
human_DMR_heart_specific_25 <- human_DMR_heart_specific_25[which(human_DMR_heart_specific_25[,4] == human_DMR_heart_specific_25[,15]),]
## 50% overlap
heart_liver_heart_lung_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_heart_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.5 -F 0.5", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3156aed87a.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31345cfccd.bed -wao -f 0.5 -F 0.5heart_liver_heart_kidney_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_heart_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.5 -F 0.5", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311ac7e706.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317c313750.bed -wao -f 0.5 -F 0.5heart_liver_liver_lung_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_liver_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.5 -F 0.5", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313ee8c25e.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31169ec12e.bed -wao -f 0.5 -F 0.5heart_liver_liver_kidney_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_liver_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.5 -F 0.5", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313f562e64.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317090084c.bed -wao -f 0.5 -F 0.5heart_liver_lung_kidney_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_lung_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.5 -F 0.5", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31730ba491.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313204bc56.bed -wao -f 0.5 -F 0.5human_heart_liver_DMR <- cbind(heart_liver_heart_lung_only_75, heart_liver_heart_kidney_only_75, heart_liver_liver_lung_only_75, heart_liver_liver_kidney_only_75, heart_liver_lung_kidney_only_75)
human_DMR_heart_specific_50 <- human_heart_liver_DMR[which(human_heart_liver_DMR[,9] > 0 & human_heart_liver_DMR[,18] > 0 & human_heart_liver_DMR[,27] < 1 & human_heart_liver_DMR[,36] < 1 & human_heart_liver_DMR[,45] < 1),]
dim(human_DMR_heart_specific_50)## [1] 2136 45human_DMR_heart_specific_50 <- human_DMR_heart_specific_50[which(human_DMR_heart_specific_50[,4] == human_DMR_heart_specific_50[,8]),]
human_DMR_heart_specific_50 <- human_DMR_heart_specific_50[which(human_DMR_heart_specific_50[,4] == human_DMR_heart_specific_50[,13]),]
human_DMR_heart_specific_50 <- human_DMR_heart_specific_50[which(human_DMR_heart_specific_50[,4] == human_DMR_heart_specific_50[,17]),]
heart_liver_heart_lung_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_heart_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311bd2c077.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31790c1619.bed -wao -f 0.75 -F 0.75heart_liver_heart_kidney_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_heart_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31416d4a81.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313759add4.bed -wao -f 0.75 -F 0.75heart_liver_liver_lung_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_liver_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31182d7808.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316b2cea75.bed -wao -f 0.75 -F 0.75heart_liver_liver_kidney_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_liver_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315137d3f6.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315cf45dfc.bed -wao -f 0.75 -F 0.75heart_liver_lung_kidney_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_lung_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316fa9a3fd.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31f3473c5.bed -wao -f 0.75 -F 0.75human_heart_liver_DMR <- cbind(heart_liver_heart_lung_only_75, heart_liver_heart_kidney_only_75, heart_liver_liver_lung_only_75, heart_liver_liver_kidney_only_75, heart_liver_lung_kidney_only_75)
human_DMR_heart_specific_75 <- human_heart_liver_DMR[which(human_heart_liver_DMR[,9] > 0 & human_heart_liver_DMR[,18] > 0 & human_heart_liver_DMR[,27] < 1 & human_heart_liver_DMR[,36] < 1 & human_heart_liver_DMR[,45] < 1),]
dim(human_DMR_heart_specific_75)## [1] 1004 45# Chimp heart-liver
# columns to pull
pull_col <- c(1:3, 16)
# make bed style format
humans_heart_liver_DMRs_bed <- chimps_heart_liver_DMRs[,pull_col]
# Get DMRs on the autosomal chromosomes only
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed[which(humans_heart_liver_DMRs_bed[,1] != "chrX"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
summary(humans_heart_liver_DMRs_bed_noX[,3] - humans_heart_liver_DMRs_bed_noX[,2])## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 5.0 266.0 498.0 617.6 849.0 4950.0humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr11_gl000202_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr17_gl000204_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
sort_chimps_heart_liver_DMRs_bed <- bedr.sort.region(humans_heart_liver_DMRs_bed_noX)## SORTING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Overlapping regions can cause unexpected results.# Chimp heart-lung
# columns to pull
pull_col <- c(1:3, 16)
# make bed style format
humans_heart_liver_DMRs_bed <- chimps_heart_lung_DMRs[,pull_col]
# Get DMRs on the autosomal chromosomes only
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed[which(humans_heart_liver_DMRs_bed[,1] != "chrX"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr11_gl000202_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr17_gl000204_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
sort_chimps_heart_lung_DMRs_bed <- bedr.sort.region(humans_heart_liver_DMRs_bed_noX)## SORTING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Overlapping regions can cause unexpected results.# chimp heart-kidney
# columns to pull
pull_col <- c(1:3, 16)
# make bed style format
humans_heart_liver_DMRs_bed <- chimps_heart_kidney_DMRs[,pull_col]
# Get DMRs on the autosomal chromosomes only
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed[which(humans_heart_liver_DMRs_bed[,1] != "chrX"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr11_gl000202_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr17_gl000204_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
summary(humans_heart_liver_DMRs_bed_noX[,3] - humans_heart_liver_DMRs_bed_noX[,2])## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 4.0 247.0 463.0 565.2 788.0 4173.0sort_chimps_heart_kidney_DMRs_bed <- bedr.sort.region(humans_heart_liver_DMRs_bed_noX, check.chr = FALSE)## SORTING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Overlapping regions can cause unexpected results.# Chimp liver-lung
# columns to pull
pull_col <- c(1:3, 16)
# make bed style format
humans_heart_liver_DMRs_bed <- chimps_liver_lung_DMRs[,pull_col]
# Get DMRs on the autosomal chromosomes only
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed[which(humans_heart_liver_DMRs_bed[,1] != "chrX"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
summary(humans_heart_liver_DMRs_bed_noX[,3] - humans_heart_liver_DMRs_bed_noX[,2])## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 5.0 247.0 459.0 577.9 793.0 5105.0humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr11_gl000202_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr17_gl000204_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
sort_chimps_liver_lung_DMRs_bed <- bedr.sort.region(humans_heart_liver_DMRs_bed_noX)## SORTING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Overlapping regions can cause unexpected results.# chimp liver-kidney
# columns to pull
pull_col <- c(1:3, 16)
# make bed style format
humans_heart_liver_DMRs_bed <- chimps_liver_kidney_DMRs[,pull_col]
# Get DMRs on the autosomal chromosomes only
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed[which(humans_heart_liver_DMRs_bed[,1] != "chrX"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
summary(humans_heart_liver_DMRs_bed_noX[,3] - humans_heart_liver_DMRs_bed_noX[,2])## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 4 245 464 571 785 4733humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr11_gl000202_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr17_gl000204_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
sort_chimps_liver_kidney_DMRs_bed <- bedr.sort.region(humans_heart_liver_DMRs_bed_noX)## SORTING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Overlapping regions can cause unexpected results.# chimp lung-kidney
# columns to pull
pull_col <- c(1:3, 16)
# make bed style format
humans_heart_liver_DMRs_bed <- chimps_lung_kidney_DMRs[,pull_col]
# Get DMRs on the autosomal chromosomes only
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed[which(humans_heart_liver_DMRs_bed[,1] != "chrX"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr11_gl000202_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr17_gl000204_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
summary(humans_heart_liver_DMRs_bed_noX[,3] - humans_heart_liver_DMRs_bed_noX[,2])## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 4.0 230.0 430.0 523.8 727.2 3703.0sort_chimps_lung_kidney_DMRs_bed <- bedr.sort.region(humans_heart_liver_DMRs_bed_noX)## SORTING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Overlapping regions can cause unexpected results.# 25% overlap
heart_liver_heart_lung_only_75 <- bedr(input = list(a = sort_chimps_heart_liver_DMRs_bed, b = sort_chimps_heart_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3130002599.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b312e06a7eb.bed -wao -f 0.25 -F 0.25heart_liver_heart_kidney_only_75 <- bedr(input = list(a = sort_chimps_heart_liver_DMRs_bed, b = sort_chimps_heart_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31483a43ce.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b314dc7394e.bed -wao -f 0.25 -F 0.25heart_liver_liver_lung_only_75 <- bedr(input = list(a = sort_chimps_heart_liver_DMRs_bed, b = sort_chimps_liver_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3139e701f4.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315b4cefc0.bed -wao -f 0.25 -F 0.25heart_liver_liver_kidney_only_75 <- bedr(input = list(a = sort_chimps_heart_liver_DMRs_bed, b = sort_chimps_liver_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313c88f0d9.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31ac2861b.bed -wao -f 0.25 -F 0.25heart_liver_lung_kidney_only_75 <- bedr(input = list(a = sort_chimps_heart_liver_DMRs_bed, b = sort_chimps_lung_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31566c261a.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b312928e3f0.bed -wao -f 0.25 -F 0.25colnames(heart_liver_heart_lung_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_heart_kidney_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_liver_lung_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_liver_kidney_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_lung_kidney_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
human_heart_liver_DMR <- left_join(heart_liver_heart_lung_only_75, heart_liver_heart_kidney_only_75, by= c("chr", "start")) %>% left_join(., heart_liver_liver_lung_only_75, by=c("chr", "start")) %>% left_join(., heart_liver_liver_kidney_only_75, by=c("chr", "start")) %>% left_join(., heart_liver_lung_kidney_only_75, by=c("chr", "start"))
chimp_DMR_heart_specific_25 <- human_heart_liver_DMR[which(human_heart_liver_DMR[,9] > 0 & human_heart_liver_DMR[,16] > 0 & human_heart_liver_DMR[,23] < 1 & human_heart_liver_DMR[,30] < 1 & human_heart_liver_DMR[,37] < 1),]
dim(chimp_DMR_heart_specific_25)## [1] 1705 37##### 50% overlap
heart_liver_heart_lung_only_75 <- bedr(input = list(a = sort_chimps_heart_liver_DMRs_bed, b = sort_chimps_heart_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.5 -F 0.5", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316c78316e.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311aaf99a1.bed -wao -f 0.5 -F 0.5heart_liver_heart_kidney_only_75 <- bedr(input = list(a = sort_chimps_heart_liver_DMRs_bed, b = sort_chimps_heart_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.5 -F 0.5", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31605263c8.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311da0f73b.bed -wao -f 0.5 -F 0.5heart_liver_liver_lung_only_75 <- bedr(input = list(a = sort_chimps_heart_liver_DMRs_bed, b = sort_chimps_liver_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.5 -F 0.5", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31351d7293.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317e28305c.bed -wao -f 0.5 -F 0.5heart_liver_liver_kidney_only_75 <- bedr(input = list(a = sort_chimps_heart_liver_DMRs_bed, b = sort_chimps_liver_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.5 -F 0.5", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3161a5fa12.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31165babf8.bed -wao -f 0.5 -F 0.5heart_liver_lung_kidney_only_75 <- bedr(input = list(a = sort_chimps_heart_liver_DMRs_bed, b = sort_chimps_lung_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.5 -F 0.5", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31a6c3b73.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3134c4c9e1.bed -wao -f 0.5 -F 0.5human_heart_liver_DMR <- cbind(heart_liver_heart_lung_only_75, heart_liver_heart_kidney_only_75, heart_liver_liver_lung_only_75, heart_liver_liver_kidney_only_75, heart_liver_lung_kidney_only_75)
chimp_DMR_heart_specific_50 <- human_heart_liver_DMR[which(human_heart_liver_DMR[,9] > 0 & human_heart_liver_DMR[,18] > 0 & human_heart_liver_DMR[,27] < 1 & human_heart_liver_DMR[,36] < 1 & human_heart_liver_DMR[,45] < 1),]
dim(chimp_DMR_heart_specific_50)## [1] 1232 45##### 75% overlap
heart_liver_heart_lung_only_75 <- bedr(input = list(a = sort_chimps_heart_liver_DMRs_bed, b = sort_chimps_heart_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b314a289bbc.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31307b315c.bed -wao -f 0.75 -F 0.75heart_liver_heart_kidney_only_75 <- bedr(input = list(a = sort_chimps_heart_liver_DMRs_bed, b = sort_chimps_heart_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b314afc9d99.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31b0c7350.bed -wao -f 0.75 -F 0.75heart_liver_liver_lung_only_75 <- bedr(input = list(a = sort_chimps_heart_liver_DMRs_bed, b = sort_chimps_liver_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313190b004.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3132378731.bed -wao -f 0.75 -F 0.75heart_liver_liver_kidney_only_75 <- bedr(input = list(a = sort_chimps_heart_liver_DMRs_bed, b = sort_chimps_liver_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b319df3921.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3116a62e4a.bed -wao -f 0.75 -F 0.75heart_liver_lung_kidney_only_75 <- bedr(input = list(a = sort_chimps_heart_liver_DMRs_bed, b = sort_chimps_lung_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3141fa179d.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3167f0be70.bed -wao -f 0.75 -F 0.75human_heart_liver_DMR <- cbind(heart_liver_heart_lung_only_75, heart_liver_heart_kidney_only_75, heart_liver_liver_lung_only_75, heart_liver_liver_kidney_only_75, heart_liver_lung_kidney_only_75)
chimp_DMR_heart_specific_75 <- human_heart_liver_DMR[which(human_heart_liver_DMR[,9] > 0 & human_heart_liver_DMR[,18] > 0 & human_heart_liver_DMR[,27] < 1 & human_heart_liver_DMR[,36] < 1 & human_heart_liver_DMR[,45] < 1),]
dim(chimp_DMR_heart_specific_75)## [1] 569 45# Chimp heart-liver
# columns to pull
pull_col <- c(1:3, 16)
# make bed style format
humans_heart_liver_DMRs_bed <- rhesus_heart_liver_DMRs[,pull_col]
# Get DMRs on the autosomal chromosomes only
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed[which(humans_heart_liver_DMRs_bed[,1] != "chrX"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
summary(humans_heart_liver_DMRs_bed_noX[,3] - humans_heart_liver_DMRs_bed_noX[,2])## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 4.0 276.2 524.0 658.6 906.0 6805.0humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr11_gl000202_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr17_gl000204_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
sort_rhesus_heart_liver_DMRs_bed <- bedr.sort.region(humans_heart_liver_DMRs_bed_noX)## SORTING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Overlapping regions can cause unexpected results.# Chimp heart-lung
# columns to pull
pull_col <- c(1:3, 16)
# make bed style format
humans_heart_liver_DMRs_bed <- rhesus_heart_lung_DMRs[,pull_col]
# Get DMRs on the autosomal chromosomes only
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed[which(humans_heart_liver_DMRs_bed[,1] != "chrX"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr11_gl000202_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr17_gl000204_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
sort_rhesus_heart_lung_DMRs_bed <- bedr.sort.region(humans_heart_liver_DMRs_bed_noX)## SORTING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Overlapping regions can cause unexpected results.# chimp heart-kidney
# columns to pull
pull_col <- c(1:3, 16)
# make bed style format
humans_heart_liver_DMRs_bed <- rhesus_heart_kidney_DMRs[,pull_col]
# Get DMRs on the autosomal chromosomes only
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed[which(humans_heart_liver_DMRs_bed[,1] != "chrX"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr11_gl000202_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr17_gl000204_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
summary(humans_heart_liver_DMRs_bed_noX[,3] - humans_heart_liver_DMRs_bed_noX[,2])## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 6.0 262.0 493.0 602.1 834.0 5515.0sort_rhesus_heart_kidney_DMRs_bed <- bedr.sort.region(humans_heart_liver_DMRs_bed_noX, check.chr = FALSE)## SORTING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Overlapping regions can cause unexpected results.# Chimp liver-lung
# columns to pull
pull_col <- c(1:3, 16)
# make bed style format
humans_heart_liver_DMRs_bed <- rhesus_liver_lung_DMRs[,pull_col]
# Get DMRs on the autosomal chromosomes only
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed[which(humans_heart_liver_DMRs_bed[,1] != "chrX"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
summary(humans_heart_liver_DMRs_bed_noX[,3] - humans_heart_liver_DMRs_bed_noX[,2])## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 5.0 265.0 498.0 629.6 856.0 6475.0humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr11_gl000202_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr17_gl000204_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
sort_rhesus_liver_lung_DMRs_bed <- bedr.sort.region(humans_heart_liver_DMRs_bed_noX)## SORTING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Overlapping regions can cause unexpected results.# chimp liver-kidney
# columns to pull
pull_col <- c(1:3, 16)
# make bed style format
humans_heart_liver_DMRs_bed <- rhesus_liver_kidney_DMRs[,pull_col]
# Get DMRs on the autosomal chromosomes only
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed[which(humans_heart_liver_DMRs_bed[,1] != "chrX"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
summary(humans_heart_liver_DMRs_bed_noX[,3] - humans_heart_liver_DMRs_bed_noX[,2])## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 4.0 269.0 508.0 635.4 879.0 5605.0humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr11_gl000202_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr17_gl000204_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
sort_rhesus_liver_kidney_DMRs_bed <- bedr.sort.region(humans_heart_liver_DMRs_bed_noX)## SORTING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Overlapping regions can cause unexpected results.# chimp lung-kidney
# columns to pull
pull_col <- c(1:3, 16)
# make bed style format
humans_heart_liver_DMRs_bed <- rhesus_lung_kidney_DMRs[,pull_col]
# Get DMRs on the autosomal chromosomes only
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed[which(humans_heart_liver_DMRs_bed[,1] != "chrX"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr11_gl000202_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
humans_heart_liver_DMRs_bed_noX <- humans_heart_liver_DMRs_bed_noX[which(humans_heart_liver_DMRs_bed_noX[,1] != "chr17_gl000204_random"),]
humans_heart_liver_DMRs_bed_noX[,1] <- as.character(humans_heart_liver_DMRs_bed_noX[,1])
humans_heart_liver_DMRs_bed_noX[,2] <- as.integer(humans_heart_liver_DMRs_bed_noX[,2])
humans_heart_liver_DMRs_bed_noX[,3] <- as.integer(humans_heart_liver_DMRs_bed_noX[,3])
summary(humans_heart_liver_DMRs_bed_noX[,3] - humans_heart_liver_DMRs_bed_noX[,2])## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 6.0 241.0 458.0 560.6 771.0 3694.0sort_rhesus_lung_kidney_DMRs_bed <- bedr.sort.region(humans_heart_liver_DMRs_bed_noX)## SORTING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Overlapping regions can cause unexpected results.# 25% overlap
heart_liver_heart_lung_only_75 <- bedr(input = list(a = sort_rhesus_heart_liver_DMRs_bed, b = sort_rhesus_heart_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31774a08ae.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b312a1af6ef.bed -wao -f 0.25 -F 0.25heart_liver_heart_kidney_only_75 <- bedr(input = list(a = sort_rhesus_heart_liver_DMRs_bed, b = sort_rhesus_heart_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31136d8933.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31522a97f7.bed -wao -f 0.25 -F 0.25heart_liver_liver_lung_only_75 <- bedr(input = list(a = sort_rhesus_heart_liver_DMRs_bed, b = sort_rhesus_liver_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3143db9e32.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311c76c6a6.bed -wao -f 0.25 -F 0.25heart_liver_liver_kidney_only_75 <- bedr(input = list(a = sort_rhesus_heart_liver_DMRs_bed, b = sort_rhesus_liver_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b314451d7f2.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3138140f5c.bed -wao -f 0.25 -F 0.25heart_liver_lung_kidney_only_75 <- bedr(input = list(a = sort_rhesus_heart_liver_DMRs_bed, b = sort_rhesus_lung_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31287658e9.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315d2fbc06.bed -wao -f 0.25 -F 0.25colnames(heart_liver_heart_lung_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_heart_kidney_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_liver_lung_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_liver_kidney_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_lung_kidney_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
human_heart_liver_DMR <- left_join(heart_liver_heart_lung_only_75, heart_liver_heart_kidney_only_75, by= c("chr", "start")) %>% left_join(., heart_liver_liver_lung_only_75, by=c("chr", "start")) %>% left_join(., heart_liver_liver_kidney_only_75, by=c("chr", "start")) %>% left_join(., heart_liver_lung_kidney_only_75, by=c("chr", "start"))
rhesus_DMR_heart_specific_25 <- human_heart_liver_DMR[which(human_heart_liver_DMR[,9] > 0 & human_heart_liver_DMR[,16] > 0 & human_heart_liver_DMR[,23] < 1 & human_heart_liver_DMR[,30] < 1 & human_heart_liver_DMR[,37] < 1),]
dim(rhesus_DMR_heart_specific_25)## [1] 1557 37heart_liver_heart_lung_only_75 <- bedr(input = list(a = sort_rhesus_heart_liver_DMRs_bed, b = sort_rhesus_heart_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.5 -F 0.5", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317e7dee2f.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3117f36f55.bed -wao -f 0.5 -F 0.5heart_liver_heart_kidney_only_75 <- bedr(input = list(a = sort_rhesus_heart_liver_DMRs_bed, b = sort_rhesus_heart_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.5 -F 0.5", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3164026ced.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317039e51b.bed -wao -f 0.5 -F 0.5heart_liver_liver_lung_only_75 <- bedr(input = list(a = sort_rhesus_heart_liver_DMRs_bed, b = sort_rhesus_liver_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.5 -F 0.5", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31421ace09.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316588a7be.bed -wao -f 0.5 -F 0.5heart_liver_liver_kidney_only_75 <- bedr(input = list(a = sort_rhesus_heart_liver_DMRs_bed, b = sort_rhesus_liver_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.5 -F 0.5", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3157140858.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317e4a2d14.bed -wao -f 0.5 -F 0.5heart_liver_lung_kidney_only_75 <- bedr(input = list(a = sort_rhesus_heart_liver_DMRs_bed, b = sort_rhesus_lung_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.5 -F 0.5", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317be28059.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b312e753cd2.bed -wao -f 0.5 -F 0.5human_heart_liver_DMR <- cbind(heart_liver_heart_lung_only_75, heart_liver_heart_kidney_only_75, heart_liver_liver_lung_only_75, heart_liver_liver_kidney_only_75, heart_liver_lung_kidney_only_75)
rhesus_DMR_heart_specific_50 <- human_heart_liver_DMR[which(human_heart_liver_DMR[,9] > 0 & human_heart_liver_DMR[,18] > 0 & human_heart_liver_DMR[,27] < 1 & human_heart_liver_DMR[,36] < 1 & human_heart_liver_DMR[,45] < 1),]
dim(rhesus_DMR_heart_specific_50)## [1] 1121 45##### 75% overlap
heart_liver_heart_lung_only_75 <- bedr(input = list(a = sort_rhesus_heart_liver_DMRs_bed, b = sort_rhesus_heart_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313763df9.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31107a7a45.bed -wao -f 0.75 -F 0.75heart_liver_heart_kidney_only_75 <- bedr(input = list(a = sort_rhesus_heart_liver_DMRs_bed, b = sort_rhesus_heart_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3115be818c.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311907f48f.bed -wao -f 0.75 -F 0.75heart_liver_liver_lung_only_75 <- bedr(input = list(a = sort_rhesus_heart_liver_DMRs_bed, b = sort_rhesus_liver_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31153143cf.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31394dea5f.bed -wao -f 0.75 -F 0.75heart_liver_liver_kidney_only_75 <- bedr(input = list(a = sort_rhesus_heart_liver_DMRs_bed, b = sort_rhesus_liver_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3141b92915.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31d3a1d16.bed -wao -f 0.75 -F 0.75heart_liver_lung_kidney_only_75 <- bedr(input = list(a = sort_rhesus_heart_liver_DMRs_bed, b = sort_rhesus_lung_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3156860068.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316b94e0e1.bed -wao -f 0.75 -F 0.75human_heart_liver_DMR <- cbind(heart_liver_heart_lung_only_75, heart_liver_heart_kidney_only_75, heart_liver_liver_lung_only_75, heart_liver_liver_kidney_only_75, heart_liver_lung_kidney_only_75)
rhesus_DMR_heart_specific_75 <- human_heart_liver_DMR[which(human_heart_liver_DMR[,9] > 0 & human_heart_liver_DMR[,18] > 0 & human_heart_liver_DMR[,27] < 1 & human_heart_liver_DMR[,36] < 1 & human_heart_liver_DMR[,45] < 1),]
dim(rhesus_DMR_heart_specific_75)## [1] 553 45### Write functions for identifying tissue-specific DMRs in a given species
# 25% overlap
tissue_specific_25_overlap <- function(DMR1_tissue_to_overlap, DMR2_tissue_to_overlap, DMR3_tissue_to_overlap, DMR4_no_overlap, DMR5_no_overlap, DMR6_no_overlap){
# Translate variables to previously-used code
sort_humans_heart_liver_DMRs_bed <- DMR1_tissue_to_overlap
sort_humans_liver_lung_DMRs_bed <- DMR2_tissue_to_overlap
sort_humans_liver_kidney_DMRs_bed <- DMR3_tissue_to_overlap
sort_humans_heart_kidney_DMRs_bed <- DMR4_no_overlap
sort_humans_heart_lung_DMRs_bed <- DMR5_no_overlap
sort_humans_lung_kidney_DMRs_bed <- DMR6_no_overlap
# Run bedtools to overlap
heart_liver_heart_lung_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_liver_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)
heart_liver_heart_kidney_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_liver_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)
heart_liver_liver_lung_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_heart_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)
heart_liver_liver_kidney_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_heart_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)
heart_liver_lung_kidney_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_lung_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)
# Convert to same name
colnames(heart_liver_heart_lung_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_heart_kidney_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_liver_lung_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_liver_kidney_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_lung_kidney_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
human_heart_liver_DMR <- left_join(heart_liver_heart_lung_only_75, heart_liver_heart_kidney_only_75, by= c("chr", "start")) %>% left_join(., heart_liver_liver_lung_only_75, by=c("chr", "start")) %>% left_join(., heart_liver_liver_kidney_only_75, by=c("chr", "start")) %>% left_join(., heart_liver_lung_kidney_only_75, by=c("chr", "start"))
DMR_tissue_specific_25 <- human_heart_liver_DMR[which(human_heart_liver_DMR[,9] > 0 & human_heart_liver_DMR[,16] > 0 & human_heart_liver_DMR[,23] < 1 & human_heart_liver_DMR[,30] < 1 & human_heart_liver_DMR[,37] < 1),]
return(DMR_tissue_specific_25)
}
# 50% overlap
tissue_specific_50_overlap <- function(DMR1_tissue_to_overlap, DMR2_tissue_to_overlap, DMR3_tissue_to_overlap, DMR4_no_overlap, DMR5_no_overlap, DMR6_no_overlap){
# Translate variables to previously-used code
sort_humans_heart_liver_DMRs_bed <- DMR1_tissue_to_overlap
sort_humans_liver_lung_DMRs_bed <- DMR2_tissue_to_overlap
sort_humans_liver_kidney_DMRs_bed <- DMR3_tissue_to_overlap
sort_humans_heart_kidney_DMRs_bed <- DMR4_no_overlap
sort_humans_heart_lung_DMRs_bed <- DMR5_no_overlap
sort_humans_lung_kidney_DMRs_bed <- DMR6_no_overlap
# Run bedtools to overlap
heart_liver_heart_lung_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_liver_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.5 -F 0.5", check.chr = FALSE)
heart_liver_heart_kidney_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_liver_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.5 -F 0.5", check.chr = FALSE)
heart_liver_liver_lung_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_heart_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.5 -F 0.5", check.chr = FALSE)
heart_liver_liver_kidney_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_heart_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.5 -F 0.5", check.chr = FALSE)
heart_liver_lung_kidney_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_lung_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.5 -F 0.5", check.chr = FALSE)
# Convert to same name
colnames(heart_liver_heart_lung_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_heart_kidney_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_liver_lung_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_liver_kidney_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_lung_kidney_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
human_heart_liver_DMR <- left_join(heart_liver_heart_lung_only_75, heart_liver_heart_kidney_only_75, by= c("chr", "start")) %>% left_join(., heart_liver_liver_lung_only_75, by=c("chr", "start")) %>% left_join(., heart_liver_liver_kidney_only_75, by=c("chr", "start")) %>% left_join(., heart_liver_lung_kidney_only_75, by=c("chr", "start"))
DMR_tissue_specific_50 <- human_heart_liver_DMR[which(human_heart_liver_DMR[,9] > 0 & human_heart_liver_DMR[,16] > 0 & human_heart_liver_DMR[,23] < 1 & human_heart_liver_DMR[,30] < 1 & human_heart_liver_DMR[,37] < 1),]
return(DMR_tissue_specific_50)
}
# 75% overlap
tissue_specific_75_overlap <- function(DMR1_tissue_to_overlap, DMR2_tissue_to_overlap, DMR3_tissue_to_overlap, DMR4_no_overlap, DMR5_no_overlap, DMR6_no_overlap){
# Translate variables to previously-used code
sort_humans_heart_liver_DMRs_bed <- DMR1_tissue_to_overlap
sort_humans_liver_lung_DMRs_bed <- DMR2_tissue_to_overlap
sort_humans_liver_kidney_DMRs_bed <- DMR3_tissue_to_overlap
sort_humans_heart_kidney_DMRs_bed <- DMR4_no_overlap
sort_humans_heart_lung_DMRs_bed <- DMR5_no_overlap
sort_humans_lung_kidney_DMRs_bed <- DMR6_no_overlap
# Run bedtools to overlap
heart_liver_heart_lung_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_liver_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)
heart_liver_heart_kidney_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_liver_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)
heart_liver_liver_lung_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_heart_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)
heart_liver_liver_kidney_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_heart_lung_DMRs_bed), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)
heart_liver_lung_kidney_only_75 <- bedr(input = list(a = sort_humans_heart_liver_DMRs_bed, b = sort_humans_lung_kidney_DMRs_bed), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)
# Convert to same name
colnames(heart_liver_heart_lung_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_heart_kidney_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_liver_lung_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_liver_kidney_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(heart_liver_lung_kidney_only_75) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
human_heart_liver_DMR <- left_join(heart_liver_heart_lung_only_75, heart_liver_heart_kidney_only_75, by= c("chr", "start")) %>% left_join(., heart_liver_liver_lung_only_75, by=c("chr", "start")) %>% left_join(., heart_liver_liver_kidney_only_75, by=c("chr", "start")) %>% left_join(., heart_liver_lung_kidney_only_75, by=c("chr", "start"))
DMR_tissue_specific_75 <- human_heart_liver_DMR[which(human_heart_liver_DMR[,9] > 0 & human_heart_liver_DMR[,16] > 0 & human_heart_liver_DMR[,23] < 1 & human_heart_liver_DMR[,30] < 1 & human_heart_liver_DMR[,37] < 1),]
return(DMR_tissue_specific_75)
}# Make a function to confirm direction. Note, this will be different for each tissue
heart_specific_direction <- function(filename_from_tissue_specific_overlap_function){
filename_from_tissue_specific_overlap_function <- filename_from_tissue_specific_overlap_function[which(filename_from_tissue_specific_overlap_function[,4] == filename_from_tissue_specific_overlap_function[,8]),]
filename_from_tissue_specific_overlap_function <- filename_from_tissue_specific_overlap_function[which(filename_from_tissue_specific_overlap_function[,4] == filename_from_tissue_specific_overlap_function[,11]),]
filename_from_tissue_specific_overlap_function <- filename_from_tissue_specific_overlap_function[which(filename_from_tissue_specific_overlap_function[,4] == filename_from_tissue_specific_overlap_function[,15]),]
return(filename_from_tissue_specific_overlap_function)
}
# Human heart specific
human_heart_specific_25 <- tissue_specific_25_overlap(sort_humans_heart_liver_DMRs_bed, sort_humans_heart_lung_DMRs_bed, sort_humans_heart_kidney_DMRs_bed, sort_humans_liver_lung_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3116bce9f4.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311ec9016.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3153831985.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313c732715.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31198e5860.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31cf8d7ad.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31464f4caf.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316f6f22c.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3174c00b62.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3139b50ed4.bed -wao -f 0.25 -F 0.25dim(human_heart_specific_25) # 2949## [1] 2949 37human_heart_specific_25 <- tissue_specific_25_overlap(sort_humans_heart_lung_DMRs_bed, sort_humans_heart_kidney_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_liver_lung_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3155969b9b.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3159aecffd.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b314a8b167b.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31d40faa3.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313902b8f1.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3166eb89de.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3119bf5c4f.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311527ca8d.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316598a0e3.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311982267d.bed -wao -f 0.25 -F 0.25dim(human_heart_specific_25) #2969## [1] 2969 37human_heart_specific_25 <- tissue_specific_25_overlap(sort_humans_heart_kidney_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_heart_lung_DMRs_bed, sort_humans_liver_lung_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317cfd358.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315af859c6.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b312a1bee13.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316507f174.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3160388a34.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3120a89080.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315425c5f8.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3178e48354.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313e549ea7.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3168cc97b2.bed -wao -f 0.25 -F 0.25dim(human_heart_specific_25) #2965## [1] 2965 37## 25% overlap
human_heart_specific_25 <- tissue_specific_25_overlap(sort_humans_heart_lung_DMRs_bed, sort_humans_heart_kidney_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_liver_lung_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b314ac601ad.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31362274f6.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31e8bf29c.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3154234bea.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b314cc5c65e.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313c20cce2.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3164726552.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317a8ee9b0.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3151916346.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31479c44cc.bed -wao -f 0.25 -F 0.25dim(human_heart_specific_25)## [1] 2969 37human_heart_specific_25 <- heart_specific_direction(human_heart_specific_25)
dim(human_heart_specific_25)## [1] 2969 37# Note: for recording #, consider using merged
#nrow(bedr.merge.region(human_DMR_heart_specific_25[,1:4]))
# 50%
human_heart_specific_50 <- tissue_specific_50_overlap(sort_humans_heart_lung_DMRs_bed, sort_humans_heart_kidney_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_liver_lung_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31159f56a3.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311217c26.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3174d080b8.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317704bc58.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31e651d58.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3128357d9a.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b312d32c083.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3149291f05.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31688d7a16.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b312ad67ab.bed -wao -f 0.5 -F 0.5dim(human_heart_specific_50)## [1] 2134 37human_heart_specific_50 <- heart_specific_direction(human_heart_specific_50)
dim(human_heart_specific_50)## [1] 2133 37# 75%
human_heart_specific_75 <- tissue_specific_75_overlap(sort_humans_heart_lung_DMRs_bed, sort_humans_heart_kidney_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_liver_lung_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313e6a93b.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316458aef9.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31648d1e97.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315617827a.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31bdabd24.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31412f941b.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316964e803.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316c329923.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311f8d87f8.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3120724e26.bed -wao -f 0.75 -F 0.75dim(human_heart_specific_75)## [1] 993 37human_heart_specific_75 <- heart_specific_direction(human_heart_specific_75)
dim(human_heart_specific_75)## [1] 993 37# Chimp heart specific- 25%
chimp_heart_specific_25 <- tissue_specific_25_overlap(sort_chimps_heart_lung_DMRs_bed, sort_chimps_heart_liver_DMRs_bed, sort_chimps_heart_kidney_DMRs_bed, sort_chimps_liver_lung_DMRs_bed, sort_chimps_liver_kidney_DMRs_bed, sort_chimps_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31314100f.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3133d82799.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3125fdf6f.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31478748f0.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31604a2e25.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311b16c80e.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311b32f10f.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b314e6aa611.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317161b353.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31664dbea3.bed -wao -f 0.25 -F 0.25dim(chimp_heart_specific_25)## [1] 1743 37# Same direction
chimp_heart_specific_25 <- heart_specific_direction(chimp_heart_specific_25)
dim(chimp_heart_specific_25)## [1] 1743 37#nrow(bedr.merge.region(chimp_DMR_heart_specific_25[,1:4]))
# Chimp heart specific- 50%
chimp_heart_specific_50 <- tissue_specific_50_overlap(sort_chimps_heart_lung_DMRs_bed, sort_chimps_heart_liver_DMRs_bed, sort_chimps_heart_kidney_DMRs_bed, sort_chimps_liver_lung_DMRs_bed, sort_chimps_liver_kidney_DMRs_bed, sort_chimps_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3127ce3872.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3134c398d.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b318906b1d.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b314295e1f4.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315c986d7e.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3131cea8e3.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31118d23cd.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31397f1f1b.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b312d665a9a.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3167062e21.bed -wao -f 0.5 -F 0.5dim(chimp_heart_specific_50)## [1] 1217 37chimp_heart_specific_50 <- heart_specific_direction(chimp_heart_specific_50)
dim(chimp_heart_specific_50)## [1] 1217 37#nrow(bedr.merge.region(chimp_DMR_heart_specific_50[,1:4]))
# Chimp heart specific- 75%
chimp_heart_specific_75 <- tissue_specific_75_overlap(sort_chimps_heart_lung_DMRs_bed, sort_chimps_heart_liver_DMRs_bed, sort_chimps_heart_kidney_DMRs_bed, sort_chimps_liver_lung_DMRs_bed, sort_chimps_liver_kidney_DMRs_bed, sort_chimps_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3122aabe87.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317710241.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313e650467.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31375c3b4a.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3130be96d0.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31526679ba.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3134df3fbd.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31681e5195.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3120b2686f.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317572d3a2.bed -wao -f 0.75 -F 0.75dim(chimp_heart_specific_75)## [1] 556 37# Same direction
chimp_heart_specific_75 <- heart_specific_direction(chimp_heart_specific_75)
dim(chimp_heart_specific_75)## [1] 556 37# Rhesus heart specific- 25%
rhesus_heart_specific_25 <- tissue_specific_25_overlap(sort_rhesus_heart_lung_DMRs_bed, sort_rhesus_heart_liver_DMRs_bed, sort_rhesus_heart_kidney_DMRs_bed, sort_rhesus_liver_lung_DMRs_bed, sort_rhesus_liver_kidney_DMRs_bed, sort_rhesus_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311612e3d0.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315170b2fc.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3170766af2.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316c337082.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3145e18e3b.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3148bba586.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b314047139.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31369e5e02.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31501a2e5f.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317fc8b6e7.bed -wao -f 0.25 -F 0.25dim(rhesus_heart_specific_25)## [1] 1598 37# Same direction
rhesus_heart_specific_25 <- heart_specific_direction(rhesus_heart_specific_25)
dim(rhesus_heart_specific_25)## [1] 1597 37# Rhesus heart specific- 50%
rhesus_heart_specific_50 <- tissue_specific_50_overlap(sort_rhesus_heart_lung_DMRs_bed, sort_rhesus_heart_liver_DMRs_bed, sort_rhesus_heart_kidney_DMRs_bed, sort_rhesus_liver_lung_DMRs_bed, sort_rhesus_liver_kidney_DMRs_bed, sort_rhesus_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316bb52480.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3169f45a4c.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31592ee892.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3160c663ae.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311da50f92.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317f24a073.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3114202fe0.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3177c819f9.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3145924561.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316c828453.bed -wao -f 0.5 -F 0.5dim(rhesus_heart_specific_50)## [1] 1148 37# Same direction
rhesus_heart_specific_50 <- heart_specific_direction(rhesus_heart_specific_50)
dim(rhesus_heart_specific_50)## [1] 1148 37# Rhesus heart specific- 75%
rhesus_heart_specific_75 <- tissue_specific_75_overlap(sort_rhesus_heart_lung_DMRs_bed, sort_rhesus_heart_liver_DMRs_bed, sort_rhesus_heart_kidney_DMRs_bed, sort_rhesus_liver_lung_DMRs_bed, sort_rhesus_liver_kidney_DMRs_bed, sort_rhesus_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3134dc86ba.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31305a6b60.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3122f2b779.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3154ea015f.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31e5957c7.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311acdb4a0.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31205a5962.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315e23cbf7.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31e14c7a6.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31680e8e2b.bed -wao -f 0.75 -F 0.75dim(rhesus_heart_specific_75)## [1] 559 37# Same direction
rhesus_heart_specific_75 <- heart_specific_direction(rhesus_heart_specific_75)
dim(rhesus_heart_specific_75)## [1] 559 37# Make a function to confirm direction. Note, this will be different for each tissue
liver_specific_direction <- function(filename_from_tissue_specific_overlap_function){
filename_from_tissue_specific_overlap_function <- filename_from_tissue_specific_overlap_function[which(filename_from_tissue_specific_overlap_function[,4] == filename_from_tissue_specific_overlap_function[,8]),]
filename_from_tissue_specific_overlap_function <- filename_from_tissue_specific_overlap_function[which(filename_from_tissue_specific_overlap_function[,4] == filename_from_tissue_specific_overlap_function[,11]),]
filename_from_tissue_specific_overlap_function <- filename_from_tissue_specific_overlap_function[which(filename_from_tissue_specific_overlap_function[,4] != filename_from_tissue_specific_overlap_function[,15]),]
return(filename_from_tissue_specific_overlap_function)
}
# Human liver specific
human_liver_specific_25 <- tissue_specific_25_overlap(sort_humans_liver_kidney_DMRs_bed, sort_humans_liver_lung_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_heart_kidney_DMRs_bed, sort_humans_heart_lung_DMRs_bed, sort_humans_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31332e1df2.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b312ce001a3.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3178684d40.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31380b7ce7.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b314d221d97.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b314f05ce1f.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3116474be1.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317816eea5.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31677abcd.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31174c6572.bed -wao -f 0.25 -F 0.25dim(human_liver_specific_25) #3276## [1] 3276 37human_liver_specific_25 <- tissue_specific_25_overlap(sort_humans_liver_lung_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_heart_kidney_DMRs_bed, sort_humans_heart_lung_DMRs_bed, sort_humans_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316a035066.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311fd84aa8.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3146a812a1.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3137766826.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316e6a3480.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b314e3a98d1.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316db2930.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315f05f2b.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3134eb5c80.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b314523ddd4.bed -wao -f 0.25 -F 0.25dim(human_liver_specific_25) #3293## [1] 3293 37human_liver_specific_25 <- tissue_specific_25_overlap(sort_humans_heart_liver_DMRs_bed, sort_humans_liver_lung_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_heart_kidney_DMRs_bed, sort_humans_heart_lung_DMRs_bed, sort_humans_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317b3b95b7.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311076202.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3125506f25.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311b7ff11b.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315485eec4.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31fecd0d6.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31310f441a.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316b5a0b30.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b314f454fc7.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3126810fa8.bed -wao -f 0.25 -F 0.25dim(human_liver_specific_25) #3280## [1] 3280 37## 25% overlap
human_liver_specific_25 <- tissue_specific_25_overlap(sort_humans_liver_lung_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_heart_kidney_DMRs_bed, sort_humans_heart_lung_DMRs_bed, sort_humans_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31281b31a9.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3142879689.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b312c46ceb8.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311e57e08.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31655c0bf7.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313d3793d1.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3174153f25.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31798e4db.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3168a7b420.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317521234e.bed -wao -f 0.25 -F 0.25dim(human_liver_specific_25)## [1] 3293 37human_liver_specific_25 <- liver_specific_direction(human_liver_specific_25)
dim(human_liver_specific_25)## [1] 3293 37# Note: for recording #, consider using merged
#nrow(bedr.merge.region(human_DMR_heart_specific_25[,1:4]))
# 50%
human_liver_specific_50 <- tissue_specific_50_overlap(sort_humans_liver_lung_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_heart_kidney_DMRs_bed, sort_humans_heart_lung_DMRs_bed, sort_humans_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3162124324.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b312f6d866a.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3143c25b4b.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311ae5c66a.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31582d557d.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3172d8faf5.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313e73df32.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31461c4ec6.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31376fa410.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3171301914.bed -wao -f 0.5 -F 0.5dim(human_liver_specific_50)## [1] 2497 37human_liver_specific_50 <- liver_specific_direction(human_liver_specific_50)
dim(human_liver_specific_50)## [1] 2497 37# 75%
human_liver_specific_75 <- tissue_specific_75_overlap(sort_humans_liver_lung_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_heart_kidney_DMRs_bed, sort_humans_heart_lung_DMRs_bed, sort_humans_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315713060.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31422f34d4.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3147109830.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316353ac84.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3173f3509.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316b1ece8e.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3138574ffb.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3162bec4a8.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313e8a57fb.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b312a0fb7fd.bed -wao -f 0.75 -F 0.75dim(human_liver_specific_75)## [1] 1323 37human_liver_specific_75 <- liver_specific_direction(human_liver_specific_75)
dim(human_liver_specific_75)## [1] 1323 37# Chimp heart specific- 25%
chimp_liver_specific_25 <- tissue_specific_25_overlap(sort_chimps_liver_lung_DMRs_bed, sort_chimps_liver_kidney_DMRs_bed, sort_chimps_heart_liver_DMRs_bed, sort_chimps_heart_kidney_DMRs_bed, sort_chimps_heart_lung_DMRs_bed, sort_chimps_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313c9416b8.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b314418e088.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31249e1334.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3114bc50ed.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316315d2d2.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3166215920.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317d319c8f.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315d0fa49f.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3178d7a446.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315a826a06.bed -wao -f 0.25 -F 0.25dim(chimp_liver_specific_25)## [1] 6377 37chimp_liver_specific_25 <- liver_specific_direction(chimp_liver_specific_25)
dim(chimp_liver_specific_25)## [1] 6377 37# Chimp heart specific- 50%
chimp_liver_specific_50 <- tissue_specific_50_overlap(sort_chimps_liver_lung_DMRs_bed, sort_chimps_liver_kidney_DMRs_bed, sort_chimps_heart_liver_DMRs_bed, sort_chimps_heart_kidney_DMRs_bed, sort_chimps_heart_lung_DMRs_bed, sort_chimps_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3126759747.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317c2150b1.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316c66dcf.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313411b3a9.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317cddd49e.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317e2eef28.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315367ddc5.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3122e3ed71.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316ce033d8.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b314e8d748a.bed -wao -f 0.5 -F 0.5dim(chimp_liver_specific_50)## [1] 4959 37chimp_liver_specific_50 <- liver_specific_direction(chimp_liver_specific_50)
dim(chimp_liver_specific_50)## [1] 4959 37# Chimp heart specific- 75%
chimp_liver_specific_75 <- tissue_specific_75_overlap(sort_chimps_liver_lung_DMRs_bed, sort_chimps_liver_kidney_DMRs_bed, sort_chimps_heart_liver_DMRs_bed, sort_chimps_heart_kidney_DMRs_bed, sort_chimps_heart_lung_DMRs_bed, sort_chimps_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316a3550b1.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31382fb633.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3137c51df7.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316bed37f8.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313183da16.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315a6e9595.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316149bb5.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313310c6e1.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3140449cd3.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317eeb615a.bed -wao -f 0.75 -F 0.75dim(chimp_liver_specific_75)## [1] 2851 37chimp_liver_specific_75 <- liver_specific_direction(chimp_liver_specific_75)
dim(chimp_liver_specific_75)## [1] 2851 37# Rhesus heart specific- 25%
rhesus_liver_specific_25 <- tissue_specific_25_overlap(sort_rhesus_liver_lung_DMRs_bed, sort_rhesus_liver_kidney_DMRs_bed, sort_rhesus_heart_liver_DMRs_bed, sort_rhesus_heart_kidney_DMRs_bed, sort_rhesus_heart_lung_DMRs_bed, sort_rhesus_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31722aa636.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3154b0fb93.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31691f47ae.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316c7cf8ed.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311092a4c3.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316eb70e6.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31711bd96.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3134fbef3f.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317c5e1b92.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3179a281ec.bed -wao -f 0.25 -F 0.25dim(rhesus_liver_specific_25)## [1] 11470 37rhesus_liver_specific_25 <- liver_specific_direction(rhesus_liver_specific_25)
dim(rhesus_liver_specific_25)## [1] 11470 37# Rhesus heart specific- 50%
rhesus_liver_specific_50 <- tissue_specific_50_overlap(sort_rhesus_liver_lung_DMRs_bed, sort_rhesus_liver_kidney_DMRs_bed, sort_rhesus_heart_liver_DMRs_bed, sort_rhesus_heart_kidney_DMRs_bed, sort_rhesus_heart_lung_DMRs_bed, sort_rhesus_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315a71d14.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315fc28850.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3119069b7b.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317ee64d1c.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b314becff30.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313c074270.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316e362634.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31700414f9.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31642fdfe5.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b314f6950c5.bed -wao -f 0.5 -F 0.5dim(rhesus_liver_specific_50)## [1] 9549 37rhesus_liver_specific_50 <- liver_specific_direction(rhesus_liver_specific_50)
dim(rhesus_liver_specific_50)## [1] 9549 37# Rhesus heart specific- 75%
rhesus_liver_specific_75 <- tissue_specific_75_overlap(sort_rhesus_liver_lung_DMRs_bed, sort_rhesus_liver_kidney_DMRs_bed, sort_rhesus_heart_liver_DMRs_bed, sort_rhesus_heart_kidney_DMRs_bed, sort_rhesus_heart_lung_DMRs_bed, sort_rhesus_lung_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316b5dc35e.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313b10263e.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b312d54f015.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311f915e83.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3135387463.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31608e1ca.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3141306e6a.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b312b44adef.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31689e9ca8.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31ad8bff1.bed -wao -f 0.75 -F 0.75dim(rhesus_liver_specific_75)## [1] 5949 37rhesus_liver_specific_75 <- liver_specific_direction(rhesus_liver_specific_75)
dim(rhesus_liver_specific_75)## [1] 5949 37# Make a function to confirm direction. Note, this will be different for each tissue
lung_specific_direction <- function(filename_from_tissue_specific_overlap_function){
filename_from_tissue_specific_overlap_function <- filename_from_tissue_specific_overlap_function[which(filename_from_tissue_specific_overlap_function[,4] != filename_from_tissue_specific_overlap_function[,8]),]
filename_from_tissue_specific_overlap_function <- filename_from_tissue_specific_overlap_function[which(filename_from_tissue_specific_overlap_function[,4] == filename_from_tissue_specific_overlap_function[,11]),]
filename_from_tissue_specific_overlap_function <- filename_from_tissue_specific_overlap_function[which(filename_from_tissue_specific_overlap_function[,4] == filename_from_tissue_specific_overlap_function[,15]),]
return(filename_from_tissue_specific_overlap_function)
}
# Human lung specific
human_lung_specific_25 <- tissue_specific_25_overlap(sort_humans_heart_lung_DMRs_bed, sort_humans_lung_kidney_DMRs_bed, sort_humans_liver_lung_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_heart_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3144ed580a.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31479142e9.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b312db8e802.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3139984bcd.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316015db21.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316ef23051.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3117d38f9.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b318ba4d6.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315e820568.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311c9996b9.bed -wao -f 0.25 -F 0.25dim(human_lung_specific_25) #479## [1] 479 37human_lung_specific_25 <- tissue_specific_25_overlap(sort_humans_lung_kidney_DMRs_bed, sort_humans_heart_lung_DMRs_bed, sort_humans_liver_lung_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_heart_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3123504a10.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316cf06b95.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3179e6f0d2.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3140c95b69.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311d1c03ed.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3143cc5833.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3123289315.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b312ecaaa99.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b314b238c93.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3169706853.bed -wao -f 0.25 -F 0.25dim(human_lung_specific_25) #469## [1] 469 37human_lung_specific_25 <- tissue_specific_25_overlap(sort_humans_liver_lung_DMRs_bed, sort_humans_lung_kidney_DMRs_bed, sort_humans_heart_lung_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_heart_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316960cdb0.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3135b06b27.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316bfb6325.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317fbe63f1.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316555bcf1.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313d77cb69.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31db704d6.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3156b9d334.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31191ec844.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31353c93c5.bed -wao -f 0.25 -F 0.25dim(human_lung_specific_25) # 464## [1] 464 37## 25% overlap
human_lung_specific_25 <- tissue_specific_25_overlap(sort_humans_heart_lung_DMRs_bed, sort_humans_lung_kidney_DMRs_bed, sort_humans_liver_lung_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_heart_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317dae714f.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313b6f4e10.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b312424af80.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3158d22461.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311f0611e3.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3160dfbf67.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b312e164491.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31d6b6068.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3179466218.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31115c164f.bed -wao -f 0.25 -F 0.25dim(human_lung_specific_25)## [1] 479 37human_lung_specific_25 <- lung_specific_direction(human_lung_specific_25)
dim(human_lung_specific_25)## [1] 479 37## 50% overlap
human_lung_specific_50 <- tissue_specific_50_overlap(sort_humans_heart_lung_DMRs_bed, sort_humans_lung_kidney_DMRs_bed, sort_humans_liver_lung_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_heart_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3135a2f6cb.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b312897c696.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3135fa31e5.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31e164120.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317d239bce.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317eadc05d.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3160b9a294.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3137784567.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313a1ed537.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31319f3619.bed -wao -f 0.5 -F 0.5dim(human_lung_specific_50)## [1] 267 37human_lung_specific_50 <- lung_specific_direction(human_lung_specific_50)
dim(human_lung_specific_50)## [1] 266 37## 75% overlap
human_lung_specific_75 <- tissue_specific_75_overlap(sort_humans_heart_lung_DMRs_bed, sort_humans_lung_kidney_DMRs_bed, sort_humans_liver_lung_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_heart_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3139ab4465.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3163e709a4.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311909fe77.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31a6d13d2.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3112c5a9e6.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31794cbb54.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31249ad634.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3149ff2987.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31309b754e.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3166132efd.bed -wao -f 0.75 -F 0.75dim(human_lung_specific_75)## [1] 84 37human_lung_specific_75 <- lung_specific_direction(human_lung_specific_75)
dim(human_lung_specific_75)## [1] 84 37## Chimp liver specific
## 25% overlap
chimp_lung_specific_25 <- tissue_specific_25_overlap(sort_chimps_heart_lung_DMRs_bed, sort_chimps_lung_kidney_DMRs_bed, sort_chimps_liver_lung_DMRs_bed, sort_chimps_heart_liver_DMRs_bed, sort_chimps_liver_kidney_DMRs_bed, sort_chimps_heart_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b312dd0acf7.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317147d14d.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311a2390e5.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3114f2dcee.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b312c4362f2.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3168098574.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b314a447d85.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b314a94b216.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3165c64783.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b318aa6297.bed -wao -f 0.25 -F 0.25dim(chimp_lung_specific_25)## [1] 454 37chimp_lung_specific_25 <- lung_specific_direction(chimp_lung_specific_25)
dim(chimp_lung_specific_25)## [1] 453 37## 50% overlap
chimp_lung_specific_50 <- tissue_specific_50_overlap(sort_chimps_heart_lung_DMRs_bed, sort_chimps_lung_kidney_DMRs_bed, sort_chimps_liver_lung_DMRs_bed, sort_chimps_heart_liver_DMRs_bed, sort_chimps_liver_kidney_DMRs_bed, sort_chimps_heart_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3173283f3c.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3132815855.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3161e9776c.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31352641e.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31f94cc.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31630df6e0.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311dad60c2.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b312613faf7.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3156e44f94.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313172cfe3.bed -wao -f 0.5 -F 0.5dim(chimp_lung_specific_50)## [1] 294 37chimp_lung_specific_50 <- lung_specific_direction(chimp_lung_specific_50)
dim(chimp_lung_specific_50)## [1] 294 37## 75% overlap
chimp_lung_specific_75 <- tissue_specific_75_overlap(sort_chimps_heart_lung_DMRs_bed, sort_chimps_lung_kidney_DMRs_bed, sort_chimps_liver_lung_DMRs_bed, sort_chimps_heart_liver_DMRs_bed, sort_chimps_liver_kidney_DMRs_bed, sort_chimps_heart_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316ea0cc40.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3124df7ab8.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313d472b4e.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31257b6c18.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3113b91a7c.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31133de43f.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313c63d50e.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317e6888ef.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3144f97171.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313b8e23a2.bed -wao -f 0.75 -F 0.75dim(chimp_lung_specific_75)## [1] 117 37chimp_lung_specific_75 <- lung_specific_direction(chimp_lung_specific_75)
dim(chimp_lung_specific_75)## [1] 117 37# Rhesus lung specific
## 25% overlap
rhesus_lung_specific_25 <- tissue_specific_25_overlap(sort_rhesus_heart_lung_DMRs_bed, sort_rhesus_lung_kidney_DMRs_bed, sort_rhesus_liver_lung_DMRs_bed, sort_rhesus_heart_liver_DMRs_bed, sort_rhesus_liver_kidney_DMRs_bed, sort_rhesus_heart_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31613b1cae.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b312c3a12d0.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3115f8b72c.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313bf2e4ee.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31162227a8.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311f69ddde.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31333cb35b.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3133b938a0.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316b81a2bf.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311ffc67a.bed -wao -f 0.25 -F 0.25dim(rhesus_lung_specific_25)## [1] 530 37rhesus_lung_specific_25 <- lung_specific_direction(rhesus_lung_specific_25)
dim(rhesus_lung_specific_25)## [1] 526 37## 50% overlap
rhesus_lung_specific_50 <- tissue_specific_50_overlap(sort_rhesus_heart_lung_DMRs_bed, sort_rhesus_lung_kidney_DMRs_bed, sort_rhesus_liver_lung_DMRs_bed, sort_rhesus_heart_liver_DMRs_bed, sort_rhesus_liver_kidney_DMRs_bed, sort_rhesus_heart_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b312de1e8a6.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315e230222.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315e8afd97.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3134935192.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3142c62b8d.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31737d18ac.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316bd5051a.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313e0f4b08.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3132fc7fb9.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31319e1974.bed -wao -f 0.5 -F 0.5dim(rhesus_lung_specific_50)## [1] 327 37rhesus_lung_specific_50 <- lung_specific_direction(rhesus_lung_specific_50)
dim(rhesus_lung_specific_50)## [1] 324 37## 75% overlap
rhesus_lung_specific_75 <- tissue_specific_75_overlap(sort_rhesus_heart_lung_DMRs_bed, sort_rhesus_lung_kidney_DMRs_bed, sort_rhesus_liver_lung_DMRs_bed, sort_rhesus_heart_liver_DMRs_bed, sort_rhesus_liver_kidney_DMRs_bed, sort_rhesus_heart_kidney_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311f874974.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3138c5e869.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3145dd72ec.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315d6b512f.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3139b2ef4f.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317e87ed2e.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3140107713.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b314cf2fa76.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317ebc3d29.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315eb96de3.bed -wao -f 0.75 -F 0.75dim(rhesus_lung_specific_75)## [1] 157 37rhesus_lung_specific_75 <- lung_specific_direction(rhesus_lung_specific_75)
dim(rhesus_lung_specific_75)## [1] 153 37# Make a function to confirm direction. Note, this will be different for each tissue
kidney_specific_direction <- function(filename_from_tissue_specific_overlap_function){
filename_from_tissue_specific_overlap_function <- filename_from_tissue_specific_overlap_function[which(filename_from_tissue_specific_overlap_function[,4] == filename_from_tissue_specific_overlap_function[,8]),]
filename_from_tissue_specific_overlap_function <- filename_from_tissue_specific_overlap_function[which(filename_from_tissue_specific_overlap_function[,4] == filename_from_tissue_specific_overlap_function[,11]),]
filename_from_tissue_specific_overlap_function <- filename_from_tissue_specific_overlap_function[which(filename_from_tissue_specific_overlap_function[,4] == filename_from_tissue_specific_overlap_function[,15]),]
return(filename_from_tissue_specific_overlap_function)
}
# Human kidney specific
human_kidney_specific_25 <- tissue_specific_25_overlap(sort_humans_lung_kidney_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_heart_kidney_DMRs_bed, sort_humans_liver_lung_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_heart_lung_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31683ac3f.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31434c6fa2.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3126735e34.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31f4f7d98.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3135fd2c5c.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313bf7c41e.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316b8b45b9.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3144682c73.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3114103c21.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3154e91b5f.bed -wao -f 0.25 -F 0.25dim(human_kidney_specific_25) # 3968## [1] 3968 37human_kidney_specific_25 <- tissue_specific_25_overlap(sort_humans_liver_kidney_DMRs_bed, sort_humans_heart_kidney_DMRs_bed, sort_humans_lung_kidney_DMRs_bed, sort_humans_liver_lung_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_heart_lung_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3190db3fd.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31723dd243.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3123e38b25.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313feef680.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3124fbe95a.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3145994666.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3141ba0861.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3143531d3b.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3121235cad.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3111f2dd75.bed -wao -f 0.25 -F 0.25dim(human_kidney_specific_25) # 3940## [1] 3940 37human_kidney_specific_25 <- tissue_specific_25_overlap(sort_humans_heart_kidney_DMRs_bed, sort_humans_lung_kidney_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_liver_lung_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_heart_lung_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311fdb3bba.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3156febbe9.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315978b71a.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31598999c5.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31686e62f3.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315aaac908.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31130ff929.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316ea81533.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3155ca15dd.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3140caaf7f.bed -wao -f 0.25 -F 0.25dim(human_kidney_specific_25) # 3962## [1] 3962 37## 25% overlap
human_kidney_specific_25 <- tissue_specific_25_overlap(sort_humans_lung_kidney_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_heart_kidney_DMRs_bed, sort_humans_liver_lung_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_heart_lung_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315e76138b.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3146f50fda.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3116d485dc.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3165996e8c.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3182da224.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315889668.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317e5bbfb5.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31a703e03.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313ed6bd9e.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316da1d03.bed -wao -f 0.25 -F 0.25dim(human_kidney_specific_25)## [1] 3968 37human_kidney_specific_25 <- kidney_specific_direction(human_kidney_specific_25)
dim(human_kidney_specific_25)## [1] 3967 37## 50% overlap
human_kidney_specific_50 <- tissue_specific_50_overlap(sort_humans_lung_kidney_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_heart_kidney_DMRs_bed, sort_humans_liver_lung_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_heart_lung_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313cb30663.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311aad4ca0.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3166e9b4e1.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313c3b737b.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315a6b8c34.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3164db3117.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31466e2ee2.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3133ab495e.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313ab8f45d.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3145cf99d4.bed -wao -f 0.5 -F 0.5dim(human_kidney_specific_50)## [1] 3018 37human_kidney_specific_50 <- kidney_specific_direction(human_kidney_specific_50)
dim(human_kidney_specific_50)## [1] 3017 37## 75% overlap
human_kidney_specific_75 <- tissue_specific_75_overlap(sort_humans_lung_kidney_DMRs_bed, sort_humans_liver_kidney_DMRs_bed, sort_humans_heart_kidney_DMRs_bed, sort_humans_liver_lung_DMRs_bed, sort_humans_heart_liver_DMRs_bed, sort_humans_heart_lung_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31539fb526.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b312d6fdc54.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b314e3b4bbb.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3124ee90ba.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3168539127.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3146119f47.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316ca67a74.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b314e6880e6.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b314cd8aeec.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317df79ecc.bed -wao -f 0.75 -F 0.75dim(human_kidney_specific_75)## [1] 1532 37human_kidney_specific_75 <- kidney_specific_direction(human_kidney_specific_75)
dim(human_kidney_specific_75)## [1] 1531 37# Chimp kidney specific
## 25% overlap
chimp_kidney_specific_25 <- tissue_specific_25_overlap(sort_chimps_lung_kidney_DMRs_bed, sort_chimps_liver_kidney_DMRs_bed, sort_chimps_heart_kidney_DMRs_bed, sort_chimps_liver_lung_DMRs_bed, sort_chimps_heart_liver_DMRs_bed, sort_chimps_heart_lung_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b318992425.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316b0ab106.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3172bb4b0.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3120ad7adf.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b314fb4fb54.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31e8b9715.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b318d5bd53.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3115633adc.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317015d160.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b312b7c2df5.bed -wao -f 0.25 -F 0.25dim(chimp_kidney_specific_25)## [1] 2304 37chimp_kidney_specific_25 <- kidney_specific_direction(chimp_kidney_specific_25)
dim(chimp_kidney_specific_25)## [1] 2302 37## 50% overlap
chimp_kidney_specific_50 <- tissue_specific_50_overlap(sort_chimps_lung_kidney_DMRs_bed, sort_chimps_liver_kidney_DMRs_bed, sort_chimps_heart_kidney_DMRs_bed, sort_chimps_liver_lung_DMRs_bed, sort_chimps_heart_liver_DMRs_bed, sort_chimps_heart_lung_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3126221967.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31216a079b.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3139090ecd.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31e42ead7.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3116f92b4e.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31286bf4da.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313265fd5b.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3120ceb606.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3128986f70.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311bd24a45.bed -wao -f 0.5 -F 0.5dim(chimp_kidney_specific_50)## [1] 1734 37chimp_kidney_specific_50 <- kidney_specific_direction(chimp_kidney_specific_50)
dim(chimp_kidney_specific_50)## [1] 1729 37## 75% overlap
chimp_kidney_specific_75 <- tissue_specific_75_overlap(sort_chimps_lung_kidney_DMRs_bed, sort_chimps_liver_kidney_DMRs_bed, sort_chimps_heart_kidney_DMRs_bed, sort_chimps_liver_lung_DMRs_bed, sort_chimps_heart_liver_DMRs_bed, sort_chimps_heart_lung_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316b7ff468.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311f3e4590.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3124114074.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31581a4409.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3118fad72e.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3159f547bb.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3137c17d76.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315cc9c10a.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3138f9d000.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317e8e6e17.bed -wao -f 0.75 -F 0.75dim(chimp_kidney_specific_75)## [1] 855 37chimp_kidney_specific_75 <- kidney_specific_direction(chimp_kidney_specific_75)
dim(chimp_kidney_specific_75)## [1] 854 37# Rhesus kidney specific
## 25% overlap
rhesus_kidney_specific_25 <- tissue_specific_25_overlap(sort_rhesus_lung_kidney_DMRs_bed, sort_rhesus_liver_kidney_DMRs_bed, sort_rhesus_heart_kidney_DMRs_bed, sort_rhesus_liver_lung_DMRs_bed, sort_rhesus_heart_liver_DMRs_bed, sort_rhesus_heart_lung_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b312ac43298.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315d45870a.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31554a2c1c.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3169f83808.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3176d718c7.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3171068f44.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3175d43c18.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31477751f5.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316b581f3d.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3138669714.bed -wao -f 0.25 -F 0.25dim(rhesus_kidney_specific_25)## [1] 3560 37rhesus_kidney_specific_25 <- kidney_specific_direction(rhesus_kidney_specific_25)
dim(rhesus_kidney_specific_25)## [1] 3555 37## 50% overlap
rhesus_kidney_specific_50 <- tissue_specific_50_overlap(sort_rhesus_lung_kidney_DMRs_bed, sort_rhesus_liver_kidney_DMRs_bed, sort_rhesus_heart_kidney_DMRs_bed, sort_rhesus_liver_lung_DMRs_bed, sort_rhesus_heart_liver_DMRs_bed, sort_rhesus_heart_lung_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3166616018.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31339e85e2.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315ee24b53.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3138747d82.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3141a81c1b.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3134b42f9.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311e473d58.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3178630056.bed -wao -f 0.5 -F 0.5
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3168961142.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31600199ab.bed -wao -f 0.5 -F 0.5dim(rhesus_kidney_specific_50)## [1] 2686 37rhesus_kidney_specific_50 <- kidney_specific_direction(rhesus_kidney_specific_50)
dim(rhesus_kidney_specific_50)## [1] 2673 37## 75% overlap
rhesus_kidney_specific_75 <- tissue_specific_75_overlap(sort_rhesus_lung_kidney_DMRs_bed, sort_rhesus_liver_kidney_DMRs_bed, sort_rhesus_heart_kidney_DMRs_bed, sort_rhesus_liver_lung_DMRs_bed, sort_rhesus_heart_liver_DMRs_bed, sort_rhesus_heart_lung_DMRs_bed)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3136621d22.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3141232961.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317c2a167c.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31773e1bd0.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31a1f03fe.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31d30d34f.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3133ccbe10.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317cd3bec6.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311185ac36.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3111daa7b4.bed -wao -f 0.75 -F 0.75dim(rhesus_kidney_specific_75)## [1] 1404 37rhesus_kidney_specific_75 <- kidney_specific_direction(rhesus_kidney_specific_75)
dim(rhesus_kidney_specific_75)## [1] 1397 37### 25% overlap
human_chimp_heart_specific_25 <- bedr(input = list(a = human_heart_specific_25[,1:4], b = chimp_heart_specific_25[,1:4]), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3110304869.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3158de5e33.bed -wao -f 0.25 -F 0.25# Human-chimp conserved
human_chimp_heart_specific_25_hs <- human_chimp_heart_specific_25[which(human_chimp_heart_specific_25[,9] == 0), ]
colnames(human_chimp_heart_specific_25_hs) <- c("chr", "start", "end")
human_chimp_heart_specific_25_conserved <- human_chimp_heart_specific_25[which(human_chimp_heart_specific_25[,9] > 0), ]
#write.table(human_chimp_heart_specific_25_hs[,1:4], "../data/human_chimp_heart_specific_25_hs.bed", quote = FALSE, row.names = FALSE, sep = "\t")
human_chimp_heart_specific_25_conserved <- human_chimp_heart_specific_25_conserved[which(human_chimp_heart_specific_25_conserved[,4] == human_chimp_heart_specific_25_conserved[,8]),]
#write.table(human_chimp_heart_specific_25_conserved[,1:4], "../data/human_chimp_heart_specific_25_conserved.bed", quote = FALSE, row.names = FALSE, sep = "\t")
# Human-chimp-rhesus
human_rhesus_heart_specific_25 <- bedr(input = list(a = human_heart_specific_25[,1:4], b = rhesus_heart_specific_25[,1:4]), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31756369cd.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3126986cc5.bed -wao -f 0.25 -F 0.25colnames(human_chimp_heart_specific_25) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(human_rhesus_heart_specific_25) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
human_chimp_rhesus_heart_specific_25 <- left_join(human_chimp_heart_specific_25, human_rhesus_heart_specific_25, by= c("chr", "start"))
# Human-chimp-rhesus conserved
human_chimp_rhesus_heart_specific_25_hs <- human_chimp_rhesus_heart_specific_25[which(human_chimp_rhesus_heart_specific_25[,9] == 0 & human_chimp_rhesus_heart_specific_25[,16] == 0), ]
#write.table(human_chimp_rhesus_heart_specific_25_hs[,1:4], "../data/human_chimp_rhesus_heart_specific_25_hs.bed", quote = FALSE, row.names = FALSE, sep = "\t")
human_chimp_rhesus_heart_specific_25_conserved <- human_chimp_rhesus_heart_specific_25[which(human_chimp_rhesus_heart_specific_25[,9] > 0 & human_chimp_rhesus_heart_specific_25[,16] > 0),]
human_chimp_rhesus_heart_specific_25_conserved <- human_chimp_rhesus_heart_specific_25_conserved[which(human_chimp_rhesus_heart_specific_25_conserved[,4] == human_chimp_rhesus_heart_specific_25_conserved[,8]),]
human_chimp_rhesus_heart_specific_25_conserved <- human_chimp_rhesus_heart_specific_25_conserved[which(human_chimp_rhesus_heart_specific_25_conserved[,11] == human_chimp_rhesus_heart_specific_25_conserved[,15]),]
#write.table(human_chimp_rhesus_heart_specific_25_conserved[,1:4], "../data/human_chimp_rhesus_heart_specific_25_conserved.bed", quote = FALSE, row.names = FALSE, sep = "\t")
# Make a Venn diagram of the overlap
### 50% overlap
human_chimp_heart_specific_50 <- bedr(input = list(a = human_DMR_heart_specific_50[,1:4], b = chimp_DMR_heart_specific_50[,1:4]), method = "intersect", params = "-wao -f 0.50 -F 0.50", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315e45429a.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3114c624d0.bed -wao -f 0.50 -F 0.50# Human-chimp conserved
human_chimp_heart_specific_50_hs <- human_chimp_heart_specific_50[which(human_chimp_heart_specific_50[,9] == 0), ]
human_chimp_heart_specific_50_conserved <- human_chimp_heart_specific_50[which(human_chimp_heart_specific_50[,9] > 0), ]
human_chimp_heart_specific_50_conserved <- human_chimp_heart_specific_50_conserved[which(human_chimp_heart_specific_50_conserved[,4] == human_chimp_heart_specific_50_conserved[,8]),]
# Human-chimp-rhesus
human_rhesus_heart_specific_50 <- bedr(input = list(a = human_DMR_heart_specific_50[,1:4], b = rhesus_DMR_heart_specific_50[,1:4]), method = "intersect", params = "-wao -f 0.50 -F 0.50", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311d135f42.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3117925759.bed -wao -f 0.50 -F 0.50human_chimp_rhesus_heart_specific_50 <- cbind(human_chimp_heart_specific_50, human_rhesus_heart_specific_50)
# Human-chimp-rhesus-conserved
human_chimp_rhesus_heart_specific_50_hs <- human_chimp_rhesus_heart_specific_50[which(human_chimp_rhesus_heart_specific_50[,9] == 0 & human_chimp_rhesus_heart_specific_50[,18] == 0), ]
human_chimp_rhesus_heart_specific_50_conserved <- human_chimp_rhesus_heart_specific_50[which(human_chimp_rhesus_heart_specific_50[,9] > 0 & human_chimp_rhesus_heart_specific_50[,18] > 0),]
human_chimp_rhesus_heart_specific_50_conserved <- human_chimp_rhesus_heart_specific_50_conserved[which(human_chimp_rhesus_heart_specific_50_conserved[,9] == human_chimp_rhesus_heart_specific_50_conserved[,18]),]
human_chimp_rhesus_heart_specific_50_conserved <- human_chimp_rhesus_heart_specific_50_conserved[which(human_chimp_rhesus_heart_specific_50_conserved[,9] == human_chimp_rhesus_heart_specific_50_conserved[,18]),]
#write.table(human_chimp_heart_specific_50_hs[,1:4], "../data/human_chimp_heart_specific_50_hs.bed", quote = FALSE, row.names = FALSE, sep = "\t")
summary(human_chimp_heart_specific_50_hs[,3]-human_chimp_heart_specific_50_hs[,2])## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 6.0 411.2 661.0 726.1 974.8 4314.0#write.table(human_chimp_heart_specific_50_conserved[,1:4], "../data/human_chimp_heart_specific_50_conserved.bed", quote = FALSE, row.names = FALSE, sep = "\t")
summary(human_chimp_heart_specific_50_conserved[,3]-human_chimp_heart_specific_50_conserved[,2])## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 105.0 679.0 933.5 967.2 1245.2 3237.0### 75% overlap
human_chimp_heart_specific_75 <- bedr(input = list(a = human_DMR_heart_specific_75[,1:4], b = chimp_DMR_heart_specific_75[,1:4]), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31302a6b01.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3155f54dc9.bed -wao -f 0.75 -F 0.75# Human-chimp conserved
human_chimp_heart_specific_75_hs <- human_chimp_heart_specific_75[which(human_chimp_heart_specific_75[,9] == 0), ]
human_chimp_heart_specific_75_conserved <- human_chimp_heart_specific_75[which(human_chimp_heart_specific_75[,9] > 0), ]
human_chimp_heart_specific_75_conserved <- human_chimp_heart_specific_75_conserved[which(human_chimp_heart_specific_75_conserved[,4] == human_chimp_heart_specific_75_conserved[,8]),]
# Human-chimp-rhesus
human_rhesus_heart_specific_75 <- bedr(input = list(a = human_DMR_heart_specific_75[,1:4], b = rhesus_DMR_heart_specific_75[,1:4]), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3168d44e80.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316d6a3277.bed -wao -f 0.75 -F 0.75human_chimp_rhesus_heart_specific_75 <- cbind(human_chimp_heart_specific_75, human_rhesus_heart_specific_75)
# Human-chimp-rhesus-conserved
human_chimp_rhesus_heart_specific_75_hs <- human_chimp_rhesus_heart_specific_75[which(human_chimp_rhesus_heart_specific_75[,9] == 0 & human_chimp_rhesus_heart_specific_75[,18] == 0), ]
human_chimp_rhesus_heart_specific_75_conserved <- human_chimp_rhesus_heart_specific_75[which(human_chimp_rhesus_heart_specific_75[,9] > 0 & human_chimp_rhesus_heart_specific_75[,18] > 0),]
dim(human_chimp_rhesus_heart_specific_75_conserved)## [1] 3 18human_chimp_rhesus_hs_versus_overlap_25 <- function(human_DMR_tissue_specific, chimp_DMR_tissue_specific, rhesus_DMR_tissue_specific, put_human_specific, put_human_chimp_conserved, put_human_specific_in_hcr, put_human_chimp_rhesus_conserved){
# Rename
human_DMR_heart_specific_25 <- human_DMR_tissue_specific[,1:4]
chimp_DMR_heart_specific_25 <- chimp_DMR_tissue_specific[,1:4]
rhesus_DMR_heart_specific_25 <- rhesus_DMR_tissue_specific[,1:4]
human_DMR_heart_specific_25 <- bedr.merge.region(human_DMR_heart_specific_25)
chimp_DMR_heart_specific_25 <- bedr.merge.region(chimp_DMR_heart_specific_25)
rhesus_DMR_heart_specific_25 <- bedr.merge.region(rhesus_DMR_heart_specific_25)
# Find the human
human_chimp_heart_specific_25 <- bedr(input = list(a = human_DMR_heart_specific_25, b = chimp_DMR_heart_specific_25), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)
human_chimp_heart_specific_25_hs <- human_chimp_heart_specific_25[which(human_chimp_heart_specific_25[,9] == 0), ]
colnames(human_chimp_heart_specific_25_hs) <- c("chr", "start", "end")
#write.table(human_chimp_heart_specific_25_hs[,1:4], put_human_specific, quote = FALSE, row.names = FALSE, sep = "\t")
# Human-chimp conserved
human_chimp_heart_specific_25_conserved <- human_chimp_heart_specific_25[which(human_chimp_heart_specific_25[,9] > 0), ]
human_chimp_heart_specific_25_conserved <- human_chimp_heart_specific_25_conserved[which(human_chimp_heart_specific_25_conserved[,4] == human_chimp_heart_specific_25_conserved[,8]),]
#write.table(human_chimp_heart_specific_25_conserved[,1:4], put_human_chimp_conserved, quote = FALSE, row.names = FALSE, sep = "\t")
# Human-chimp-rhesus
human_rhesus_heart_specific_25 <- bedr(input = list(a = human_DMR_heart_specific_25[,1:4], b = rhesus_DMR_heart_specific_25[,1:4]), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)
colnames(human_chimp_heart_specific_25) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(human_rhesus_heart_specific_25) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
human_chimp_rhesus_heart_specific_25 <- left_join(human_chimp_heart_specific_25, human_rhesus_heart_specific_25, by= c("chr", "start"))
# Human-chimp-rhesus conserved
human_chimp_rhesus_heart_specific_25_hs <- human_chimp_rhesus_heart_specific_25[which(human_chimp_rhesus_heart_specific_25[,9] == 0 & human_chimp_rhesus_heart_specific_25[,16] == 0), ]
#write.table(human_chimp_rhesus_heart_specific_25_hs[,1:4], put_human_specific_in_hcr, quote = FALSE, row.names = FALSE, sep = "\t")
human_chimp_rhesus_heart_specific_25_conserved <- human_chimp_rhesus_heart_specific_25[which(human_chimp_rhesus_heart_specific_25[,9] > 0 & human_chimp_rhesus_heart_specific_25[,16] > 0),]
human_chimp_rhesus_heart_specific_25_conserved <- human_chimp_rhesus_heart_specific_25_conserved[which(human_chimp_rhesus_heart_specific_25_conserved[,4] == human_chimp_rhesus_heart_specific_25_conserved[,8]),]
human_chimp_rhesus_heart_specific_25_conserved <- human_chimp_rhesus_heart_specific_25_conserved[which(human_chimp_rhesus_heart_specific_25_conserved[,11] == human_chimp_rhesus_heart_specific_25_conserved[,15]),]
#write.table(human_chimp_rhesus_heart_specific_25_conserved[,1:4], put_human_chimp_rhesus_conserved, quote = FALSE, row.names = FALSE, sep = "\t")
row_numbers <- cbind(nrow(human_chimp_heart_specific_25_hs), nrow(human_chimp_heart_specific_25_conserved), nrow(human_chimp_rhesus_heart_specific_25_hs), nrow(human_chimp_rhesus_heart_specific_25_conserved))
return(row_numbers)
}
# 50% overlap
human_chimp_rhesus_hs_versus_overlap_50 <- function(human_DMR_tissue_specific, chimp_DMR_tissue_specific, rhesus_DMR_tissue_specific, put_human_specific, put_human_chimp_conserved, put_human_specific_in_hcr, put_human_chimp_rhesus_conserved){
# Rename
human_DMR_heart_specific_25 <- human_DMR_tissue_specific[,1:4]
chimp_DMR_heart_specific_25 <- chimp_DMR_tissue_specific[,1:4]
rhesus_DMR_heart_specific_25 <- rhesus_DMR_tissue_specific[,1:4]
human_DMR_heart_specific_25 <- bedr.merge.region(human_DMR_heart_specific_25)
chimp_DMR_heart_specific_25 <- bedr.merge.region(chimp_DMR_heart_specific_25)
rhesus_DMR_heart_specific_25 <- bedr.merge.region(rhesus_DMR_heart_specific_25)
# Find the human
human_chimp_heart_specific_25 <- bedr(input = list(a = human_DMR_heart_specific_25, b = chimp_DMR_heart_specific_25), method = "intersect", params = "-wao -f 0.50 -F 0.50", check.chr = FALSE)
human_chimp_heart_specific_25_hs <- human_chimp_heart_specific_25[which(human_chimp_heart_specific_25[,9] == 0), ]
colnames(human_chimp_heart_specific_25_hs) <- c("chr", "start", "end")
#write.table(human_chimp_heart_specific_25_hs[,1:4], put_human_specific, quote = FALSE, row.names = FALSE, sep = "\t")
# Human-chimp conserved
human_chimp_heart_specific_25_conserved <- human_chimp_heart_specific_25[which(human_chimp_heart_specific_25[,9] > 0), ]
human_chimp_heart_specific_25_conserved <- human_chimp_heart_specific_25_conserved[which(human_chimp_heart_specific_25_conserved[,4] == human_chimp_heart_specific_25_conserved[,8]),]
#write.table(human_chimp_heart_specific_25_conserved[,1:4], put_human_chimp_conserved, quote = FALSE, row.names = FALSE, sep = "\t")
# Human-chimp-rhesus
human_rhesus_heart_specific_25 <- bedr(input = list(a = human_DMR_heart_specific_25[,1:4], b = rhesus_DMR_heart_specific_25[,1:4]), method = "intersect", params = "-wao -f 0.50 -F 0.50", check.chr = FALSE)
colnames(human_chimp_heart_specific_25) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(human_rhesus_heart_specific_25) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
human_chimp_rhesus_heart_specific_25 <- left_join(human_chimp_heart_specific_25, human_rhesus_heart_specific_25, by= c("chr", "start"))
# Human-chimp-rhesus conserved
human_chimp_rhesus_heart_specific_25_hs <- human_chimp_rhesus_heart_specific_25[which(human_chimp_rhesus_heart_specific_25[,9] == 0 & human_chimp_rhesus_heart_specific_25[,16] == 0), ]
#write.table(human_chimp_rhesus_heart_specific_25_hs[,1:4], put_human_specific_in_hcr, quote = FALSE, row.names = FALSE, sep = "\t")
human_chimp_rhesus_heart_specific_25_conserved <- human_chimp_rhesus_heart_specific_25[which(human_chimp_rhesus_heart_specific_25[,9] > 0 & human_chimp_rhesus_heart_specific_25[,16] > 0),]
human_chimp_rhesus_heart_specific_25_conserved <- human_chimp_rhesus_heart_specific_25_conserved[which(human_chimp_rhesus_heart_specific_25_conserved[,4] == human_chimp_rhesus_heart_specific_25_conserved[,8]),]
human_chimp_rhesus_heart_specific_25_conserved <- human_chimp_rhesus_heart_specific_25_conserved[which(human_chimp_rhesus_heart_specific_25_conserved[,11] == human_chimp_rhesus_heart_specific_25_conserved[,15]),]
#write.table(human_chimp_rhesus_heart_specific_25_conserved[,1:4], put_human_chimp_rhesus_conserved, quote = FALSE, row.names = FALSE, sep = "\t")
row_numbers <- cbind(nrow(human_chimp_heart_specific_25_hs), nrow(human_chimp_heart_specific_25_conserved), nrow(human_chimp_rhesus_heart_specific_25_hs), nrow(human_chimp_rhesus_heart_specific_25_conserved))
return(row_numbers)
}
# 75% overlap
human_chimp_rhesus_hs_versus_overlap_75 <- function(human_DMR_tissue_specific, chimp_DMR_tissue_specific, rhesus_DMR_tissue_specific, put_human_specific, put_human_chimp_conserved, put_human_specific_in_hcr, put_human_chimp_rhesus_conserved){
# Rename
human_DMR_heart_specific_25 <- human_DMR_tissue_specific[,1:4]
chimp_DMR_heart_specific_25 <- chimp_DMR_tissue_specific[,1:4]
rhesus_DMR_heart_specific_25 <- rhesus_DMR_tissue_specific[,1:4]
human_DMR_heart_specific_25 <- bedr.merge.region(human_DMR_heart_specific_25)
chimp_DMR_heart_specific_25 <- bedr.merge.region(chimp_DMR_heart_specific_25)
rhesus_DMR_heart_specific_25 <- bedr.merge.region(rhesus_DMR_heart_specific_25)
# Find the human
human_chimp_heart_specific_25 <- bedr(input = list(a = human_DMR_heart_specific_25, b = chimp_DMR_heart_specific_25), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)
human_chimp_heart_specific_25_hs <- human_chimp_heart_specific_25[which(human_chimp_heart_specific_25[,9] == 0), ]
colnames(human_chimp_heart_specific_25_hs) <- c("chr", "start", "end")
#write.table(human_chimp_heart_specific_25_hs[,1:4], put_human_specific, quote = FALSE, row.names = FALSE, sep = "\t")
# Human-chimp conserved
human_chimp_heart_specific_25_conserved <- human_chimp_heart_specific_25[which(human_chimp_heart_specific_25[,9] > 0), ]
human_chimp_heart_specific_25_conserved <- human_chimp_heart_specific_25_conserved[which(human_chimp_heart_specific_25_conserved[,4] == human_chimp_heart_specific_25_conserved[,8]),]
#write.table(human_chimp_heart_specific_25_conserved[,1:4], put_human_chimp_conserved, quote = FALSE, row.names = FALSE, sep = "\t")
# Human-chimp-rhesus
human_rhesus_heart_specific_25 <- bedr(input = list(a = human_DMR_heart_specific_25[,1:4], b = rhesus_DMR_heart_specific_25[,1:4]), method = "intersect", params = "-wao -f 0.75 -F 0.75", check.chr = FALSE)
colnames(human_chimp_heart_specific_25) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(human_rhesus_heart_specific_25) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
human_chimp_rhesus_heart_specific_25 <- left_join(human_chimp_heart_specific_25, human_rhesus_heart_specific_25, by= c("chr", "start"))
# Human-chimp-rhesus conserved
human_chimp_rhesus_heart_specific_25_hs <- human_chimp_rhesus_heart_specific_25[which(human_chimp_rhesus_heart_specific_25[,9] == 0 & human_chimp_rhesus_heart_specific_25[,16] == 0), ]
#write.table(human_chimp_rhesus_heart_specific_25_hs[,1:4], put_human_specific_in_hcr, quote = FALSE, row.names = FALSE, sep = "\t")
human_chimp_rhesus_heart_specific_25_conserved <- human_chimp_rhesus_heart_specific_25[which(human_chimp_rhesus_heart_specific_25[,9] > 0 & human_chimp_rhesus_heart_specific_25[,16] > 0),]
human_chimp_rhesus_heart_specific_25_conserved <- human_chimp_rhesus_heart_specific_25_conserved[which(human_chimp_rhesus_heart_specific_25_conserved[,4] == human_chimp_rhesus_heart_specific_25_conserved[,8]),]
human_chimp_rhesus_heart_specific_25_conserved <- human_chimp_rhesus_heart_specific_25_conserved[which(human_chimp_rhesus_heart_specific_25_conserved[,11] == human_chimp_rhesus_heart_specific_25_conserved[,15]),]
#write.table(human_chimp_rhesus_heart_specific_25_conserved[,1:4], put_human_chimp_rhesus_conserved, quote = FALSE, row.names = FALSE, sep = "\t")
row_numbers <- cbind(nrow(human_chimp_heart_specific_25_hs), nrow(human_chimp_heart_specific_25_conserved), nrow(human_chimp_rhesus_heart_specific_25_hs), nrow(human_chimp_rhesus_heart_specific_25_conserved))
return(row_numbers)
}# Heart specific
human_chimp_rhesus_hs_versus_overlap_25(human_heart_specific_25, chimp_heart_specific_25, rhesus_heart_specific_25, "../data/overlap_reg/human_chimp_heart_specific_25_hs.bed", "../data/overlap_reg/human_chimp_heart_specific_25_conserved.bed", "../data/overlap_reg/human_chimp_rhesus_heart_specific_25_hs.bed", "../data/overlap_reg/human_chimp_rhesus_heart_specific_25_conserved.bed")## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b31441bbcf5.bed -d 0 -c 4 -o collapse
## * Collapsing 2969 --> 2964 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b3134afda00.bed -d 0 -c 4 -o collapse
## * Collapsing 1743 --> 1741 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b3133de6383.bed -d 0 -c 4 -o collapse
## * Collapsing 1597 --> 1594 regions... NOTE
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b314c3496aa.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311ae8b931.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3120e0e7d.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316c8ec1b1.bed -wao -f 0.25 -F 0.25## [,1] [,2] [,3] [,4]
## [1,] 2509 455 2411 69human_chimp_rhesus_hs_versus_overlap_50(human_heart_specific_50, chimp_heart_specific_50, rhesus_heart_specific_50, "../data/overlap_reg/human_chimp_heart_specific_50_hs.bed", "../data/overlap_reg/human_chimp_heart_specific_50_conserved.bed", "../data/overlap_reg/human_chimp_rhesus_heart_specific_50_hs.bed", "../data/overlap_reg/human_chimp_rhesus_heart_specific_50_conserved.bed")## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b311283fa80.bed -d 0 -c 4 -o collapse
## * Collapsing 2133 --> 2133 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b313e6f4efd.bed -d 0 -c 4 -o collapse
## * Collapsing 1217 --> 1217 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b315e6316e4.bed -d 0 -c 4 -o collapse
## * Collapsing 1148 --> 1148 regions... NOTE
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3139ad598f.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b312ceac51b.bed -wao -f 0.50 -F 0.50
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3177acc004.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311fbabdfd.bed -wao -f 0.50 -F 0.50## [,1] [,2] [,3] [,4]
## [1,] 1874 259 1821 41human_chimp_rhesus_hs_versus_overlap_75(human_heart_specific_75, chimp_heart_specific_75, rhesus_heart_specific_75, "../data/overlap_reg/human_chimp_heart_specific_75_hs.bed", "../data/overlap_reg/human_chimp_heart_specific_75_conserved.bed", "../data/overlap_reg/human_chimp_rhesus_heart_specific_75_hs.bed", "../data/overlap_reg/human_chimp_rhesus_heart_specific_75_conserved.bed")## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b3153829fbe.bed -d 0 -c 4 -o collapse
## * Collapsing 993 --> 993 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b3129f986ad.bed -d 0 -c 4 -o collapse
## * Collapsing 556 --> 556 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b31768e6c33.bed -d 0 -c 4 -o collapse
## * Collapsing 559 --> 559 regions... NOTE
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31175ec19.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311e8f76d4.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3154159d33.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31aee6294.bed -wao -f 0.75 -F 0.75## [,1] [,2] [,3] [,4]
## [1,] 947 46 932 3# Liver specific
human_chimp_rhesus_hs_versus_overlap_25(human_liver_specific_25, chimp_liver_specific_25, rhesus_liver_specific_25, "../data/overlap_reg/human_chimp_liver_specific_25_hs.bed", "../data/overlap_reg/human_chimp_liver_specific_25_conserved.bed", "../data/overlap_reg/human_chimp_rhesus_liver_specific_25_hs.bed", "../data/overlap_reg/human_chimp_rhesus_liver_specific_25_conserved.bed")## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b3175e86d3b.bed -d 0 -c 4 -o collapse
## * Collapsing 3293 --> 3278 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b3137629714.bed -d 0 -c 4 -o collapse
## * Collapsing 6377 --> 6361 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b31c0bc70c.bed -d 0 -c 4 -o collapse
## * Collapsing 11470 --> 11433 regions... NOTE
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317265e78f.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316d9ef20e.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31513318ae.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b314aa1aab4.bed -wao -f 0.25 -F 0.25## [,1] [,2] [,3] [,4]
## [1,] 1952 1333 1585 516human_chimp_rhesus_hs_versus_overlap_50(human_liver_specific_50, chimp_liver_specific_50, rhesus_liver_specific_50, "../data/overlap_reg/human_chimp_liver_specific_50_hs.bed", "../data/overlap_reg/human_chimp_liver_specific_50_conserved.bed", "../data/overlap_reg/human_chimp_rhesus_liver_specific_50_hs.bed", "../data/overlap_reg/human_chimp_rhesus_liver_specific_50_conserved.bed")## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b315f279971.bed -d 0 -c 4 -o collapse
## * Collapsing 2497 --> 2497 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b316e054294.bed -d 0 -c 4 -o collapse
## * Collapsing 4959 --> 4959 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b313a3a011b.bed -d 0 -c 4 -o collapse
## * Collapsing 9549 --> 9549 regions... NOTE
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316a352245.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3169a3a993.bed -wao -f 0.50 -F 0.50
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b312990d76d.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31ad71e2c.bed -wao -f 0.50 -F 0.50## [,1] [,2] [,3] [,4]
## [1,] 1725 772 1510 233human_chimp_rhesus_hs_versus_overlap_75(human_liver_specific_75, chimp_liver_specific_75, rhesus_liver_specific_75, "../data/overlap_reg/human_chimp_liver_specific_75_hs.bed", "../data/overlap_reg/human_chimp_liver_specific_75_conserved.bed", "../data/overlap_reg/human_chimp_rhesus_liver_specific_75_hs.bed", "../data/overlap_reg/human_chimp_rhesus_liver_specific_75_conserved.bed")## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b316b8e67d5.bed -d 0 -c 4 -o collapse
## * Collapsing 1323 --> 1323 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b312ec9d21c.bed -d 0 -c 4 -o collapse
## * Collapsing 2851 --> 2851 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b312f28ad96.bed -d 0 -c 4 -o collapse
## * Collapsing 5949 --> 5949 regions... NOTE
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3147f81a2d.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317f70c5ab.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3118eee586.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31a5789f2.bed -wao -f 0.75 -F 0.75## [,1] [,2] [,3] [,4]
## [1,] 1111 212 1063 25# Lung specific
human_chimp_rhesus_hs_versus_overlap_25(human_lung_specific_25, chimp_lung_specific_25, rhesus_lung_specific_25, "../data/overlap_reg/human_chimp_lung_specific_25_hs.bed", "../data/overlap_reg/human_chimp_lung_specific_25_conserved.bed", "../data/overlap_reg/human_chimp_rhesus_lung_specific_25_hs.bed", "../data/overlap_reg/human_chimp_rhesus_lung_specific_25_conserved.bed")## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b31351f12e.bed -d 0 -c 4 -o collapse
## * Collapsing 479 --> 478 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b312dac44fa.bed -d 0 -c 4 -o collapse
## * Collapsing 453 --> 452 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b3155cb8d04.bed -d 0 -c 4 -o collapse
## * Collapsing 526 --> 524 regions... NOTE
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31af8ff06.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b312dfcb228.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31403d66e6.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313422fcab.bed -wao -f 0.25 -F 0.25## [,1] [,2] [,3] [,4]
## [1,] 427 51 415 6human_chimp_rhesus_hs_versus_overlap_50(human_lung_specific_50, chimp_lung_specific_50, rhesus_lung_specific_50, "../data/overlap_reg/human_chimp_lung_specific_50_hs.bed", "../data/overlap_reg/human_chimp_lung_specific_50_conserved.bed", "../data/overlap_reg/human_chimp_rhesus_lung_specific_50_hs.bed", "../data/overlap_reg/human_chimp_rhesus_lung_specific_50_conserved.bed")## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b316ffc3d10.bed -d 0 -c 4 -o collapse
## * Collapsing 266 --> 266 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b312c6610f9.bed -d 0 -c 4 -o collapse
## * Collapsing 294 --> 294 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b3131eb759e.bed -d 0 -c 4 -o collapse
## * Collapsing 324 --> 324 regions... NOTE
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317d47152f.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3116be9d87.bed -wao -f 0.50 -F 0.50
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31261ad4d0.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311134f1bd.bed -wao -f 0.50 -F 0.50## [,1] [,2] [,3] [,4]
## [1,] 243 23 240 2human_chimp_rhesus_hs_versus_overlap_75(human_lung_specific_75, chimp_lung_specific_75, rhesus_lung_specific_75, "../data/overlap_reg/human_chimp_lung_specific_75_hs.bed", "../data/overlap_reg/human_chimp_lung_specific_75_conserved.bed", "../data/overlap_reg/human_chimp_rhesus_lung_specific_75_hs.bed", "../data/overlap_reg/human_chimp_rhesus_lung_specific_75_conserved.bed")## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b3117ddcf95.bed -d 0 -c 4 -o collapse
## * Collapsing 84 --> 84 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b311289d90c.bed -d 0 -c 4 -o collapse
## * Collapsing 117 --> 117 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b31616a4e6d.bed -d 0 -c 4 -o collapse
## * Collapsing 153 --> 153 regions... NOTE
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3139543abf.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3179b88fcc.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3154dc0a01.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31c12f388.bed -wao -f 0.75 -F 0.75## [,1] [,2] [,3] [,4]
## [1,] 83 1 83 0# Kidney specific
human_chimp_rhesus_hs_versus_overlap_25(human_kidney_specific_25, chimp_kidney_specific_25, rhesus_kidney_specific_25, "../data/overlap_reg/human_chimp_kidney_specific_25_hs.bed", "../data/overlap_reg/human_chimp_kidney_specific_25_conserved.bed", "../data/overlap_reg/human_chimp_rhesus_kidney_specific_25_hs.bed", "../data/overlap_reg/human_chimp_rhesus_kidney_specific_25_conserved.bed")## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b313e4aa6b7.bed -d 0 -c 4 -o collapse
## * Collapsing 3967 --> 3957 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b316337fe9b.bed -d 0 -c 4 -o collapse
## * Collapsing 2302 --> 2300 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b312a04dd0c.bed -d 0 -c 4 -o collapse
## * Collapsing 3555 --> 3547 regions... NOTE
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315f760a7.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317f8439c6.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315aca2767.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31570f7f7a.bed -wao -f 0.25 -F 0.25## [,1] [,2] [,3] [,4]
## [1,] 3063 897 2772 299human_chimp_rhesus_hs_versus_overlap_50(human_kidney_specific_50, chimp_kidney_specific_50, rhesus_kidney_specific_50, "../data/overlap_reg/human_chimp_kidney_specific_50_hs.bed", "../data/overlap_reg/human_chimp_kidney_specific_50_conserved.bed", "../data/overlap_reg/human_chimp_rhesus_kidney_specific_50_hs.bed", "../data/overlap_reg/human_chimp_rhesus_kidney_specific_50_conserved.bed")## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b3133e84bc9.bed -d 0 -c 4 -o collapse
## * Collapsing 3017 --> 3017 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b316fb4cbf7.bed -d 0 -c 4 -o collapse
## * Collapsing 1729 --> 1729 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b311e9588bb.bed -d 0 -c 4 -o collapse
## * Collapsing 2673 --> 2673 regions... NOTE
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3159679425.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316a566949.bed -wao -f 0.50 -F 0.50
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b312584b0fb.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31342903de.bed -wao -f 0.50 -F 0.50## [,1] [,2] [,3] [,4]
## [1,] 2472 545 2279 141human_chimp_rhesus_hs_versus_overlap_75(human_kidney_specific_75, chimp_kidney_specific_75, rhesus_kidney_specific_75, "../data/overlap_reg/human_chimp_kidney_specific_75_hs.bed", "../data/overlap_reg/human_chimp_kidney_specific_75_conserved.bed", "../data/overlap_reg/human_chimp_rhesus_kidney_specific_75_hs.bed", "../data/overlap_reg/human_chimp_rhesus_kidney_specific_75_conserved.bed")## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b317ed5d11.bed -d 0 -c 4 -o collapse
## * Collapsing 1531 --> 1531 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b311acb6721.bed -d 0 -c 4 -o collapse
## * Collapsing 854 --> 854 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b3117f5d55c.bed -d 0 -c 4 -o collapse
## * Collapsing 1397 --> 1397 regions... NOTE
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31119a6cd3.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3125261706.bed -wao -f 0.75 -F 0.75
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31661d6bf9.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b312fa36b01.bed -wao -f 0.75 -F 0.75## [,1] [,2] [,3] [,4]
## [1,] 1388 143 1341 19tissue_conserved_25_overlap <- function(DMR1_human, DMR1_chimp, DMR1_rhesus){
# Human-chimp/human-rhesus
human_chimp_DMR <- bedr(input = list(a = DMR1_human, b = DMR1_chimp), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)
human_chimp_DMR <- human_chimp_DMR[which(human_chimp_DMR[,6] != -1), ]
human_rhesus_DMR <- bedr(input = list(a = DMR1_human, b = DMR1_rhesus), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)
human_rhesus_DMR <- human_rhesus_DMR[which(human_rhesus_DMR[,6] != -1), ]
chimp_rhesus_DMR <- bedr(input = list(a = DMR1_chimp, b = DMR1_rhesus), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)
chimp_rhesus_DMR <- chimp_rhesus_DMR[which(chimp_rhesus_DMR[,6] != -1), ]
colnames(human_chimp_DMR) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(human_rhesus_DMR) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
colnames(chimp_rhesus_DMR) <- c("chr", "start", "end", "direction", "chr.b", "start.b", "end.b", "direction.b", "overlap")
human_chimp_DMR <- bedr.merge.region(human_chimp_DMR)
human_rhesus_DMR <- bedr.merge.region(human_rhesus_DMR)
chimp_rhesus_DMR <- bedr.merge.region(chimp_rhesus_DMR)
# Human-chimp-rhesus
human_chimp_rhesus1_DMR <- bedr(input = list(a = human_chimp_DMR, b = human_rhesus_DMR), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)
human_chimp_rhesus1a_DMR <- human_chimp_rhesus1_DMR[which(human_chimp_rhesus1_DMR[,6] != -1), ]
human_chimp_rhesus2_DMR <- bedr(input = list(a = human_chimp_rhesus1a_DMR[,1:4], b = chimp_rhesus_DMR), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)
human_chimp_rhesus2a_DMR <- human_chimp_rhesus2_DMR[which(human_chimp_rhesus2_DMR[,6] != -1), ]
nrow(human_chimp_rhesus2a_DMR)
# human_chimp_rhesus2a_DMR gives the number of H/C/R conserved tDMRs
# Conserved in only 2 species
human_chimp_only <- bedr(input = list(a = human_chimp_DMR, b = human_chimp_rhesus2a_DMR[,1:4]), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)
human_chimp_only <- human_chimp_only[which(human_chimp_only[,6] == -1), ]
nrow(human_chimp_only)
human_rhesus_only <- bedr(input = list(a = human_rhesus_DMR, b = human_chimp_rhesus2a_DMR[,1:4]), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)
human_rhesus_only <- human_rhesus_only[which(human_rhesus_only[,6] == -1), ]
nrow(human_rhesus_only)
chimp_rhesus_only <- bedr(input = list(a = chimp_rhesus_DMR, b = human_chimp_rhesus2a_DMR[,1:4]), method = "intersect", params = "-wao -f 0.25 -F 0.25", check.chr = FALSE)
chimp_rhesus_only <- chimp_rhesus_only[which(chimp_rhesus_only[,6] == -1), ]
nrow(chimp_rhesus_only)
# Species-specific
human_specific <- nrow(DMR1_human) - nrow(human_chimp_only) - nrow(human_rhesus_only) - nrow(human_chimp_rhesus2a_DMR)
chimp_specific <- nrow(DMR1_chimp) - nrow(human_chimp_only) - nrow(chimp_rhesus_only) - nrow(human_chimp_rhesus2a_DMR)
rhesus_specific <- nrow(DMR1_rhesus) - nrow(human_rhesus_only) - nrow(chimp_rhesus_only) - nrow(human_chimp_rhesus2a_DMR)
combine <- cbind(human_specific, chimp_specific, rhesus_specific, nrow(human_chimp_only), nrow(human_rhesus_only), nrow(chimp_rhesus_only), nrow(human_chimp_rhesus2a_DMR))
colnames(combine) <- c("human_specific", "chimp_specific", "rhesus_specific", "hc", "hr", "cr", "hcr_conserved")
return(combine)
}
tissue_conserved_25_overlap(human_heart_specific_25[,1:4], chimp_heart_specific_25[,1:4], rhesus_heart_specific_25[,1:4])## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3171620842.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31767f9167.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3111fe2bc3.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317bd78ecb.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315e58ce95.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3177e0359b.bed -wao -f 0.25 -F 0.25
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b31358e3dab.bed -d 0 -c 4 -o collapse
## * Collapsing 457 --> 455 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b3168de3628.bed -d 0 -c 4 -o collapse
## * Collapsing 168 --> 167 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b3164b15639.bed -d 0 -c 4 -o collapse
## * Collapsing 142 --> 142 regions... NOTE
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b314f14e07e.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3155a15d0.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b312bbf7bb1.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31290028a4.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b318a79717.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31178da31a.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31a06bfab.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31334fcee3.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3148b15ef9.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b314515240b.bed -wao -f 0.25 -F 0.25## human_specific chimp_specific rhesus_specific hc hr cr
## [1,] 2413 1212 1354 389 101 76
## hcr_conserved
## [1,] 66# human_specific chimp_specific rhesus_specific hc hr cr hcr_conserved
#[1,] 2413 1212 1354 389 101 76 66
human_heart_specific_25_hypo <- human_heart_specific_25[which(human_heart_specific_25[,4] == "hypo"),]
chimp_heart_specific_25_hypo <- chimp_heart_specific_25[which(chimp_heart_specific_25[,4] == "hypo"),]
rhesus_heart_specific_25_hypo <- rhesus_heart_specific_25[which(rhesus_heart_specific_25[,4] == "hypo"),]
tissue_conserved_25_overlap(human_heart_specific_25_hypo[,1:4], chimp_heart_specific_25_hypo[,1:4], rhesus_heart_specific_25_hypo[,1:4])## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315b32edde.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311497d98c.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31d84e7bd.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3153ad7f47.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315a8fc9af.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316fea5477.bed -wao -f 0.25 -F 0.25
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b31cef13e4.bed -d 0 -c 4 -o collapse
## * Collapsing 414 --> 413 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b3139dee9ca.bed -d 0 -c 4 -o collapse
## * Collapsing 155 --> 154 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b31124a93b8.bed -d 0 -c 4 -o collapse
## * Collapsing 128 --> 128 regions... NOTE
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3142d10514.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31665f62d2.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31eb84cbd.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3114026121.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b316cfc003d.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31fb99357.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3125f17cd.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b314beea1c6.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b314fe217df.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31b75430c.bed -wao -f 0.25 -F 0.25## human_specific chimp_specific rhesus_specific hc hr cr hcr_conserved
## [1,] 2094 1014 1175 351 92 66 62# human_specific chimp_specific rhesus_specific hc hr cr hcr_conserved
#[1,] 2094 1014 1175 351 92 66 62
dev.off()## null device
## 1draw.triple.venn(nrow(human_heart_specific_25_hypo), nrow(chimp_heart_specific_25_hypo), nrow(rhesus_heart_specific_25_hypo), 351+62, 66+62, 92+62, 62, main= "Heart versus kidney (hypomethylated)", category = c("Human", "Chimp", "Rhesus macaque"), height=3000, width=3000, cex=2 , fill = pal[1:3], lty=1, cat.cex = 2, main.cex = 2)## (polygon[GRID.polygon.1], polygon[GRID.polygon.2], polygon[GRID.polygon.3], polygon[GRID.polygon.4], polygon[GRID.polygon.5], polygon[GRID.polygon.6], text[GRID.text.7], text[GRID.text.8], text[GRID.text.9], text[GRID.text.10], text[GRID.text.11], text[GRID.text.12], text[GRID.text.13], text[GRID.text.14], text[GRID.text.15], text[GRID.text.16])human_heart_specific_25_hypo <- human_heart_specific_25[which(human_heart_specific_25[,4] == "hyper"),]
chimp_heart_specific_25_hypo <- chimp_heart_specific_25[which(chimp_heart_specific_25[,4] == "hyper"),]
rhesus_heart_specific_25_hypo <- rhesus_heart_specific_25[which(rhesus_heart_specific_25[,4] == "hyper"),]
tissue_conserved_25_overlap(human_heart_specific_25_hypo[,1:4], chimp_heart_specific_25_hypo[,1:4], rhesus_heart_specific_25_hypo[,1:4])## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3175ae4893.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31337edd1f.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313b2c4e08.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316169a88d.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313634a289.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b318b6147b.bed -wao -f 0.25 -F 0.25
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b3144047cc7.bed -d 0 -c 4 -o collapse
## * Collapsing 43 --> 42 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b3153caf3c2.bed -d 0 -c 4 -o collapse
## * Collapsing 13 --> 13 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b314c7b09ff.bed -d 0 -c 4 -o collapse
## * Collapsing 14 --> 14 regions... NOTE
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317e15d3d5.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31375bf7e5.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31760a6746.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31786fc210.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31418ee386.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b312950220b.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3170e0a135.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31ce5b469.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3124ba4222.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31685f4c4e.bed -wao -f 0.25 -F 0.25## human_specific chimp_specific rhesus_specific hc hr cr hcr_conserved
## [1,] 319 198 179 38 9 10 4# human_specific chimp_specific rhesus_specific hc hr cr hcr_conserved
#[1,] 319 198 179 38 9 10 4
dev.off()## null device
## 1draw.triple.venn(nrow(human_heart_specific_25_hypo), nrow(chimp_heart_specific_25_hypo), nrow(rhesus_heart_specific_25_hypo), 38+4, 10+4, 9+4, 4, main= "Heart versus kidney (hypomethylated)", category = c("Human", "Chimp", "Rhesus macaque"), height=3000, width=3000, cex=2 , fill = pal[1:3], lty=1, cat.cex = 2, main.cex = 2)## (polygon[GRID.polygon.17], polygon[GRID.polygon.18], polygon[GRID.polygon.19], polygon[GRID.polygon.20], polygon[GRID.polygon.21], polygon[GRID.polygon.22], text[GRID.text.23], text[GRID.text.24], text[GRID.text.25], text[GRID.text.26], text[GRID.text.27], text[GRID.text.28], text[GRID.text.29], text[GRID.text.30], text[GRID.text.31], text[GRID.text.32])tissue_conserved_25_overlap(human_liver_specific_25[,1:4], chimp_liver_specific_25[,1:4], rhesus_liver_specific_25[,1:4])## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311aab5489.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311a1c787e.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3138e39d23.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3145850ec2.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3154e9679f.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313e498fda.bed -wao -f 0.25 -F 0.25
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b31364541e0.bed -d 0 -c 4 -o collapse
## * Collapsing 1349 --> 1326 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b31608340e3.bed -d 0 -c 4 -o collapse
## * Collapsing 891 --> 872 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Bedtools requires sorted input for merging!
## Your data is being automatically sorted
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b3112b773b1.bed -d 0 -c 4 -o collapse
## * Collapsing 1349 --> 1315 regions... NOTE
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3140e76f5b.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316e163e2d.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3167fa973c.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b316b7ba7f6.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3152bba16d.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3134ef8270.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3130b868ac.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b312a6881bd.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3167e73130.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315fd76f6b.bed -wao -f 0.25 -F 0.25## human_specific chimp_specific rhesus_specific hc hr cr
## [1,] 1571 4207 9754 849 395 843
## hcr_conserved
## [1,] 478# human_specific chimp_specific rhesus_specific hc hr cr hcr_conserved
#[1,] 1571 4207 9754 849 395 843 478
tissue_conserved_25_overlap(human_lung_specific_25[,1:4], chimp_lung_specific_25[,1:4], rhesus_lung_specific_25[,1:4])## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31a6170b1.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313aae6be1.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311882a33e.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3110412ddb.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315e4382a.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b313ea971f6.bed -wao -f 0.25 -F 0.25
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b31d3812fa.bed -d 0 -c 4 -o collapse
## * Collapsing 52 --> 51 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b3124cfa38f.bed -d 0 -c 4 -o collapse
## * Collapsing 19 --> 18 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b3160e8f029.bed -d 0 -c 4 -o collapse
## * Collapsing 26 --> 25 regions... NOTE
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317d57e2c4.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3144acaf20.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311fce0117.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b315dd384c8.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31575f3439.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317d8d5794.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b315d50d7c1.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b314bf61801.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317dd79743.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31255b8167.bed -wao -f 0.25 -F 0.25## human_specific chimp_specific rhesus_specific hc hr cr hcr_conserved
## [1,] 415 382 488 46 13 20 5# human_specific chimp_specific rhesus_specific hc hr cr hcr_conserved
#[1,] 415 382 488 46 13 20 5
tissue_conserved_25_overlap(human_kidney_specific_25[,1:4], chimp_kidney_specific_25[,1:4], rhesus_kidney_specific_25[,1:4])## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b31625d20a1.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b317046d2ea.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b311bda3b69.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3129018c2d.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input seems to be in bed format but chr/start/end column names are missing
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... FAIL
## The input for object has overlapping features!
## This can cause unexpected results for some set operations.
## i.e. x <- bedr.merge.region(x)
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b317fa50edc.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31189c5dfb.bed -wao -f 0.25 -F 0.25
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b315b8e13cc.bed -d 0 -c 4 -o collapse
## * Collapsing 902 --> 894 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b3139cfd937.bed -d 0 -c 4 -o collapse
## * Collapsing 599 --> 587 regions... NOTE
## MERGING
## VALIDATE REGIONS
## * Checking input type... PASS
## Input is in bed format
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Processing input (1): i
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## bedtools merge -i /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/i_10b31f76b00c.bed -d 0 -c 4 -o collapse
## * Collapsing 440 --> 434 regions... NOTE
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313e267ec6.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b311a4e8be1.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b314476674.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3159837906.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b313caeabb2.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b3175833652.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3132212c87.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31626b42f3.bed -wao -f 0.25 -F 0.25
## * Processing input (1): a
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## * Processing input (2): b
## CONVERT TO BED
## * Checking input type... PASS
## Input is in bed format
## VALIDATE REGIONS
## * Check if index is a string... PASS
## * Check index pattern... PASS
## * Check for missing values... PASS
## * Check for larger start position... PASS.
## * Check if zero based... PASS
## * Checking sort order... PASS
## * Checking for overlapping 'contiguous' regions... PASS
## bedtools intersect -a /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/a_10b3143f9b072.bed -b /var/folders/rf/qrcw6ncj05z1pc_pq9xzw3540000gn/T//RtmpP81HHD/b_10b31760df7bc.bed -wao -f 0.25 -F 0.25## human_specific chimp_specific rhesus_specific hc hr cr
## [1,] 2773 1260 2820 607 300 148
## hcr_conserved
## [1,] 287Left ventricle (E095), liver (E066), and lung (E096) from http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/ucsc_compatible/ Kidney from http://egg2.wustl.edu/roadmap/data/byFileType/peaks/unconsolidated/broadPeak/ucsc_compatible/
bedtools intersect -a human_chimp_heart_specific_25_hs.bed -b E095-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_heart_specific_25_hs_test.bed
bedtools intersect -a human_chimp_heart_specific_25_conserved.bed -b E095-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_heart_specific_25_conserved_test.bed
bedtools intersect -a human_chimp_rhesus_lung_specific_25_conserved.bed -b E095-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_heart_specific_25_conserved_H3K27_HEART.bed
bedtools intersect -a human_chimp_rhesus_lung_specific_25_conserved.bed -b BI.Adult_Kidney.H3K27ac.27.broadPeak -wao -f 0.25 > human_chimp_heart_specific_25_conserved_H3K27_KIDNEY.bed
bedtools intersect -a human_chimp_rhesus_lung_specific_25_conserved.bed -b E066-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_heart_specific_25_conserved_H3K27_LIVER.bed
bedtools intersect -a human_chimp_rhesus_lung_specific_25_conserved.bed -b E096-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_heart_specific_25_conserved_H3K27_LUNGS.bed
bedtools intersect -a human_chimp_rhesus_heart_specific_25_conserved.bed -b ENCSR501FWC_rep2_1_pe_bwa_biorep_filtered_hotspots.bed -wao -f 0.25 > human_chimp_heart_specific_25_conserved_DHS_HEART.bed
bedtools intersect -a human_chimp_rhesus_heart_specific_25_conserved.bed -b ENCSR422PVL_rep1_2_se_bwa_biorep_filtered_hotspots.bed -wao -f 0.25 > human_chimp_heart_specific_25_conserved_DHS_KIDNEY.bed
bedtools intersect -a human_chimp_rhesus_heart_specific_25_conserved.bed -b ENCSR562FNN_rep1_1_pe_bwa_biorep_filtered_hotspots.bed -wao -f 0.25 > human_chimp_heart_specific_25_conserved_DHS_LIVER.bed
bedtools intersect -a human_chimp_rhesus_heart_specific_25_conserved.bed -b ENCSR541AVF_rep1_3_se_bwa_biorep_filtered_hotspots.bed -wao -f 0.25 > human_chimp_heart_specific_25_conserved_DHS_LUNGS.bed
# Read in data- human specific
human_chimp_heart_specific_25_hs_test <- read.delim("../data/overlap_reg/human_chimp_heart_specific_25_conserved_DHS_HEART.bed", header = FALSE)
dim(human_chimp_heart_specific_25_hs_test)## [1] 72 14# Eliminate duplicates
dedup_human_chimp_heart_specific_25_hs_test <- human_chimp_heart_specific_25_hs_test[!duplicated(human_chimp_heart_specific_25_hs_test[,1:2]),]
dim(dedup_human_chimp_heart_specific_25_hs_test)## [1] 69 14dedup_overlap_human_chimp_heart_specific_25_hs_test <- dedup_human_chimp_heart_specific_25_hs_test[which(dedup_human_chimp_heart_specific_25_hs_test$V6 != -1),]
# Look at fraction overlapping H3K27ac
location <- dedup_human_chimp_heart_specific_25_hs_test[which(dedup_human_chimp_heart_specific_25_hs_test$V6 != -1),]
nrow(location)/nrow(human_chimp_heart_specific_25_hs_test)## [1] 0.6388889#0.6388889
hyper_only_conserved <- human_chimp_heart_specific_25_hs_test[which(human_chimp_heart_specific_25_hs_test[,4] == "hypo"),]
hyper_only_conserved_overlap <- hyper_only_conserved[which(hyper_only_conserved$V6 != -1),]
nrow(hyper_only_conserved_overlap)/nrow(hyper_only_conserved)## [1] 0.7058824nrow(hyper_only_conserved_overlap)## [1] 48human_chimp_heart_specific_25_hs_test <- read.delim("../data/overlap_reg/human_chimp_heart_specific_25_conserved_DHS_KIDNEY.bed", header = FALSE)
dim(human_chimp_heart_specific_25_hs_test)## [1] 69 14# Eliminate duplicates
dedup_human_chimp_heart_specific_25_hs_test <- human_chimp_heart_specific_25_hs_test[!duplicated(human_chimp_heart_specific_25_hs_test[,1:2]),]
dim(dedup_human_chimp_heart_specific_25_hs_test)## [1] 69 14dedup_overlap_human_chimp_heart_specific_25_hs_test <- dedup_human_chimp_heart_specific_25_hs_test[which(dedup_human_chimp_heart_specific_25_hs_test$V6 != -1),]
# Look at fraction overlapping H3K27ac
location <- dedup_human_chimp_heart_specific_25_hs_test[which(dedup_human_chimp_heart_specific_25_hs_test$V6 != -1),]
nrow(location)/nrow(human_chimp_heart_specific_25_hs_test)## [1] 0hyper_only_conserved <- human_chimp_heart_specific_25_hs_test[which(human_chimp_heart_specific_25_hs_test[,4] == "hypo"),]
hyper_only_conserved_overlap <- hyper_only_conserved[which(hyper_only_conserved$V6 != -1),]
nrow(hyper_only_conserved_overlap)/nrow(hyper_only_conserved)## [1] 0nrow(hyper_only_conserved_overlap)## [1] 0# 0.115
human_chimp_heart_specific_25_hs_test <- read.delim("../data/overlap_reg/human_chimp_heart_specific_25_conserved_DHS_LIVER.bed", header = FALSE)
dim(human_chimp_heart_specific_25_hs_test)## [1] 69 14# Eliminate duplicates
dedup_human_chimp_heart_specific_25_hs_test <- human_chimp_heart_specific_25_hs_test[!duplicated(human_chimp_heart_specific_25_hs_test[,1:2]),]
dim(dedup_human_chimp_heart_specific_25_hs_test)## [1] 69 14dedup_overlap_human_chimp_heart_specific_25_hs_test <- dedup_human_chimp_heart_specific_25_hs_test[which(dedup_human_chimp_heart_specific_25_hs_test$V6 != -1),]
# Look at fraction overlapping H3K27ac
location <- dedup_human_chimp_heart_specific_25_hs_test[which(dedup_human_chimp_heart_specific_25_hs_test$V6 != -1),]
nrow(location)/nrow(human_chimp_heart_specific_25_hs_test)## [1] 0.115942# 0.115 8/69
hyper_only_conserved <- human_chimp_heart_specific_25_hs_test[which(human_chimp_heart_specific_25_hs_test[,4] == "hypo"),]
hyper_only_conserved_overlap <- hyper_only_conserved[which(hyper_only_conserved$V6 != -1),]
nrow(hyper_only_conserved_overlap)/nrow(hyper_only_conserved)## [1] 0.1230769nrow(hyper_only_conserved_overlap)## [1] 8human_chimp_heart_specific_25_hs_test <- read.delim("../data/overlap_reg/human_chimp_heart_specific_25_conserved_DHS_LUNGS.bed", header = FALSE)
dim(human_chimp_heart_specific_25_hs_test)## [1] 69 14# Eliminate duplicates
dedup_human_chimp_heart_specific_25_hs_test <- human_chimp_heart_specific_25_hs_test[!duplicated(human_chimp_heart_specific_25_hs_test[,1:2]),]
dim(dedup_human_chimp_heart_specific_25_hs_test)## [1] 69 14dedup_overlap_human_chimp_heart_specific_25_hs_test <- dedup_human_chimp_heart_specific_25_hs_test[which(dedup_human_chimp_heart_specific_25_hs_test$V6 != -1),]
# Look at fraction overlapping H3K27ac
location <- dedup_human_chimp_heart_specific_25_hs_test[which(dedup_human_chimp_heart_specific_25_hs_test$V6 != -1),]
nrow(location)/nrow(human_chimp_heart_specific_25_hs_test)## [1] 0.1014493#0.1014493 #7
hyper_only_conserved <- human_chimp_heart_specific_25_hs_test[which(human_chimp_heart_specific_25_hs_test[,4] == "hypo"),]
hyper_only_conserved_overlap <- hyper_only_conserved[which(hyper_only_conserved$V6 != -1),]
nrow(hyper_only_conserved_overlap)/nrow(hyper_only_conserved)## [1] 0.1076923nrow(hyper_only_conserved_overlap)## [1] 7# Read in data- human specific
human_chimp_heart_specific_25_hs_test <- read.delim("../data/overlap_reg/human_chimp_heart_specific_25_conserved_H3K27_HEART.bed", header = FALSE)
dim(human_chimp_heart_specific_25_hs_test)## [1] 6 14# Eliminate duplicates
dedup_human_chimp_heart_specific_25_hs_test <- human_chimp_heart_specific_25_hs_test[!duplicated(human_chimp_heart_specific_25_hs_test[,1:2]),]
dim(dedup_human_chimp_heart_specific_25_hs_test)## [1] 6 14dedup_overlap_human_chimp_heart_specific_25_hs_test <- dedup_human_chimp_heart_specific_25_hs_test[which(dedup_human_chimp_heart_specific_25_hs_test$V6 != -1),]
# Look at fraction overlapping H3K27ac
location <- dedup_human_chimp_heart_specific_25_hs_test[which(dedup_human_chimp_heart_specific_25_hs_test$V6 != -1),]
nrow(location)/nrow(human_chimp_heart_specific_25_hs_test)## [1] 0.1666667#0.8550725 59/69
hyper_only_conserved <- human_chimp_heart_specific_25_hs_test[which(human_chimp_heart_specific_25_hs_test[,4] == "hypo"),]
hyper_only_conserved_overlap <- hyper_only_conserved[which(hyper_only_conserved$V6 != -1),]
nrow(hyper_only_conserved_overlap)/nrow(hyper_only_conserved)## [1] NaNnrow(hyper_only_conserved_overlap)## [1] 0human_chimp_heart_specific_25_hs_test <- read.delim("../data/overlap_reg/human_chimp_heart_specific_25_conserved_H3K27_KIDNEY.bed", header = FALSE)
dim(human_chimp_heart_specific_25_hs_test)## [1] 6 14# Eliminate duplicates
dedup_human_chimp_heart_specific_25_hs_test <- human_chimp_heart_specific_25_hs_test[!duplicated(human_chimp_heart_specific_25_hs_test[,1:2]),]
dim(dedup_human_chimp_heart_specific_25_hs_test)## [1] 6 14dedup_overlap_human_chimp_heart_specific_25_hs_test <- dedup_human_chimp_heart_specific_25_hs_test[which(dedup_human_chimp_heart_specific_25_hs_test$V6 != -1),]
# Look at fraction overlapping H3K27ac
location <- dedup_human_chimp_heart_specific_25_hs_test[which(dedup_human_chimp_heart_specific_25_hs_test$V6 != -1),]
nrow(location)/nrow(human_chimp_heart_specific_25_hs_test)## [1] 0.5hyper_only_conserved <- human_chimp_heart_specific_25_hs_test[which(human_chimp_heart_specific_25_hs_test[,4] == "hypo"),]
hyper_only_conserved_overlap <- hyper_only_conserved[which(hyper_only_conserved$V6 != -1),]
nrow(hyper_only_conserved_overlap)/nrow(hyper_only_conserved)## [1] NaNnrow(hyper_only_conserved_overlap)## [1] 0# 0.71 49
human_chimp_heart_specific_25_hs_test <- read.delim("../data/overlap_reg/human_chimp_heart_specific_25_conserved_H3K27_LIVER.bed", header = FALSE)
dim(human_chimp_heart_specific_25_hs_test)## [1] 6 14# Eliminate duplicates
dedup_human_chimp_heart_specific_25_hs_test <- human_chimp_heart_specific_25_hs_test[!duplicated(human_chimp_heart_specific_25_hs_test[,1:2]),]
dim(dedup_human_chimp_heart_specific_25_hs_test)## [1] 6 14dedup_overlap_human_chimp_heart_specific_25_hs_test <- dedup_human_chimp_heart_specific_25_hs_test[which(dedup_human_chimp_heart_specific_25_hs_test$V6 != -1),]
# Look at fraction overlapping H3K27ac
location <- dedup_human_chimp_heart_specific_25_hs_test[which(dedup_human_chimp_heart_specific_25_hs_test$V6 != -1),]
nrow(location)/nrow(human_chimp_heart_specific_25_hs_test)## [1] 0.3333333# 0.5652174 39
hyper_only_conserved <- human_chimp_heart_specific_25_hs_test[which(human_chimp_heart_specific_25_hs_test[,4] == "hypo"),]
hyper_only_conserved_overlap <- hyper_only_conserved[which(hyper_only_conserved$V6 != -1),]
nrow(hyper_only_conserved_overlap)/nrow(hyper_only_conserved)## [1] NaNnrow(hyper_only_conserved_overlap)## [1] 0human_chimp_heart_specific_25_hs_test <- read.delim("../data/overlap_reg/human_chimp_heart_specific_25_conserved_H3K27_LUNGS.bed", header = FALSE)
dim(human_chimp_heart_specific_25_hs_test)## [1] 6 14# Eliminate duplicates
dedup_human_chimp_heart_specific_25_hs_test <- human_chimp_heart_specific_25_hs_test[!duplicated(human_chimp_heart_specific_25_hs_test[,1:2]),]
dim(dedup_human_chimp_heart_specific_25_hs_test)## [1] 6 14dedup_overlap_human_chimp_heart_specific_25_hs_test <- dedup_human_chimp_heart_specific_25_hs_test[which(dedup_human_chimp_heart_specific_25_hs_test$V6 != -1),]
# Look at fraction overlapping H3K27ac
location <- dedup_human_chimp_heart_specific_25_hs_test[which(dedup_human_chimp_heart_specific_25_hs_test$V6 != -1),]
nrow(location)/nrow(human_chimp_heart_specific_25_hs_test)## [1] 0.5#0.7246377 #50
hyper_only_conserved <- human_chimp_heart_specific_25_hs_test[which(human_chimp_heart_specific_25_hs_test[,4] == "hypo"),]
hyper_only_conserved_overlap <- hyper_only_conserved[which(hyper_only_conserved$V6 != -1),]
nrow(hyper_only_conserved_overlap)/nrow(hyper_only_conserved)## [1] NaNnrow(hyper_only_conserved_overlap)## [1] 0prop.test(x = c(8,48), n = c(65,65))##
## 2-sample test for equality of proportions with continuity
## correction
##
## data: c(8, 48) out of c(65, 65)
## X-squared = 47.715, df = 1, p-value = 4.93e-12
## alternative hypothesis: two.sided
## 95 percent confidence interval:
## -0.7641587 -0.4666105
## sample estimates:
## prop 1 prop 2
## 0.1230769 0.7384615bedtools intersect -a human_chimp_heart_specific_25_hs.bed -b E095-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_heart_specific_25_hs_test.bed
bedtools intersect -a human_chimp_heart_specific_25_conserved.bed -b E095-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_heart_specific_25_conserved_test.bed
bedtools intersect -a human_chimp_heart_specific_25_hs.bed -b E096-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_heart_specific_25_hs_liver_test.bed
bedtools intersect -a human_chimp_heart_specific_25_conserved.bed -b E096-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_heart_specific_25_conserved_liver_test.bed
bedtools intersect -a human_chimp_rhesus_heart_specific_25_hs.bed -b E095-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_rhesus_heart_specific_25_hs_test.bed
bedtools intersect -a human_chimp_rhesus_heart_specific_25_conserved.bed -b E095-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_rhesus_heart_specific_25_conserved_test.bed
bedtools intersect -a human_chimp_heart_specific_50_hs.bed -b E095-H3K27ac.broadPeak -wao -f 0.50 > human_chimp_heart_specific_50_hs_test.bed bedtools intersect -a human_chimp_heart_specific_50_conserved.bed -b E095-H3K27ac.broadPeak -wao -f 0.50 > human_chimp_heart_specific_50_conserved_test.bed bedtools intersect -a human_chimp_rhesus_heart_specific_50_hs.bed -b E095-H3K27ac.broadPeak -wao -f 0.50 > human_chimp_rhesus_heart_specific_50_hs_test.bed bedtools intersect -a human_chimp_rhesus_heart_specific_50_conserved.bed -b E095-H3K27ac.broadPeak -wao -f 0.50 > human_chimp_rhesus_heart_specific_50_conserved_test.bed
bedtools intersect -a human_chimp_heart_specific_75_hs.bed -b E095-H3K27ac.broadPeak -wao -f 0.75 > human_chimp_heart_specific_75_hs_test.bed bedtools intersect -a human_chimp_heart_specific_75_conserved.bed -b E095-H3K27ac.broadPeak -wao -f 0.75 > human_chimp_heart_specific_75_conserved_test.bed bedtools intersect -a human_chimp_rhesus_heart_specific_75_hs.bed -b E095-H3K27ac.broadPeak -wao -f 0.75 > human_chimp_rhesus_heart_specific_75_hs_test.bed bedtools intersect -a human_chimp_rhesus_heart_specific_75_conserved.bed -b E095-H3K27ac.broadPeak -wao -f 0.75 > human_chimp_rhesus_heart_specific_75_conserved_test.bed
bedtools intersect -a human_chimp_liver_specific_25_hs.bed -b E066-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_liver_specific_25_hs_test.bed bedtools intersect -a human_chimp_liver_specific_25_conserved.bed -b E066-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_liver_specific_25_conserved_test.bed
bedtools intersect -a human_chimp_liver_specific_25_hs.bed -b E096-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_liver_specific_25_hs_lung_test.bed bedtools intersect -a human_chimp_liver_specific_25_conserved.bed -b E096-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_liver_specific_25_conserved_lung_test.bed
bedtools intersect -a human_chimp_rhesus_liver_specific_25_hs.bed -b E066-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_rhesus_liver_specific_25_hs_test.bed bedtools intersect -a human_chimp_rhesus_liver_specific_25_conserved.bed -b E066-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_rhesus_liver_specific_25_conserved_test.bed
bedtools intersect -a human_chimp_liver_specific_50_hs.bed -b E066-H3K27ac.broadPeak -wao -f 0.50 > human_chimp_liver_specific_50_hs_test.bed bedtools intersect -a human_chimp_liver_specific_50_conserved.bed -b E066-H3K27ac.broadPeak -wao -f 0.50 > human_chimp_liver_specific_50_conserved_test.bed bedtools intersect -a human_chimp_rhesus_liver_specific_50_hs.bed -b E066-H3K27ac.broadPeak -wao -f 0.50 > human_chimp_rhesus_liver_specific_50_hs_test.bed bedtools intersect -a human_chimp_rhesus_liver_specific_50_conserved.bed -b E066-H3K27ac.broadPeak -wao -f 0.50 > human_chimp_rhesus_liver_specific_50_conserved_test.bed
bedtools intersect -a human_chimp_liver_specific_75_hs.bed -b E066-H3K27ac.broadPeak -wao -f 0.75 > human_chimp_liver_specific_75_hs_test.bed bedtools intersect -a human_chimp_liver_specific_75_conserved.bed -b E066-H3K27ac.broadPeak -wao -f 0.75 > human_chimp_liver_specific_75_conserved_test.bed bedtools intersect -a human_chimp_rhesus_liver_specific_75_hs.bed -b E066-H3K27ac.broadPeak -wao -f 0.75 > human_chimp_rhesus_liver_specific_75_hs_test.bed bedtools intersect -a human_chimp_rhesus_liver_specific_75_conserved.bed -b E066-H3K27ac.broadPeak -wao -f 0.75 > human_chimp_rhesus_liver_specific_75_conserved_test.bed
bedtools intersect -a human_chimp_lung_specific_25_hs.bed -b E096-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_lung_specific_25_hs_test.bed bedtools intersect -a human_chimp_lung_specific_25_conserved.bed -b E096-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_lung_specific_25_conserved_test.bed
bedtools intersect -a human_chimp_lung_specific_25_hs.bed -b E095-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_lung_specific_25_hs_heart_test.bed bedtools intersect -a human_chimp_lung_specific_25_conserved.bed -b E095-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_lung_specific_25_conserved_heart_test.bed
bedtools intersect -a human_chimp_rhesus_lung_specific_25_hs.bed -b E096-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_rhesus_lung_specific_25_hs_test.bed bedtools intersect -a human_chimp_rhesus_lung_specific_25_conserved.bed -b E096-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_rhesus_lung_specific_25_conserved_test.bed
bedtools intersect -a human_chimp_lung_specific_50_hs.bed -b E096-H3K27ac.broadPeak -wao -f 0.50 > human_chimp_lung_specific_50_hs_test.bed bedtools intersect -a human_chimp_lung_specific_50_conserved.bed -b E096-H3K27ac.broadPeak -wao -f 0.50 > human_chimp_lung_specific_50_conserved_test.bed bedtools intersect -a human_chimp_rhesus_lung_specific_50_hs.bed -b E096-H3K27ac.broadPeak -wao -f 0.50 > human_chimp_rhesus_lung_specific_50_hs_test.bed bedtools intersect -a human_chimp_rhesus_lung_specific_50_conserved.bed -b E096-H3K27ac.broadPeak -wao -f 0.50 > human_chimp_rhesus_lung_specific_50_conserved_test.bed
bedtools intersect -a human_chimp_lung_specific_75_hs.bed -b E096-H3K27ac.broadPeak -wao -f 0.75 > human_chimp_lung_specific_75_hs_test.bed bedtools intersect -a human_chimp_lung_specific_75_conserved.bed -b E096-H3K27ac.broadPeak -wao -f 0.75 > human_chimp_lung_specific_75_conserved_test.bed bedtools intersect -a human_chimp_rhesus_lung_specific_75_hs.bed -b E096-H3K27ac.broadPeak -wao -f 0.75 > human_chimp_rhesus_lung_specific_75_hs_test.bed bedtools intersect -a human_chimp_rhesus_lung_specific_75_conserved.bed -b E096-H3K27ac.broadPeak -wao -f 0.75 > human_chimp_rhesus_lung_specific_75_conserved_test.bed
bedtools intersect -a human_chimp_kidney_specific_25_hs.bed -b BI.Adult_Kidney.H3K27ac.27.broadPeak -wao -f 0.25 > human_chimp_kidney_specific_25_hs_test.bed bedtools intersect -a human_chimp_kidney_specific_25_conserved.bed -b BI.Adult_Kidney.H3K27ac.27.broadPeak -wao -f 0.25 > human_chimp_kidney_specific_25_conserved_test.bed
bedtools intersect -a human_chimp_kidney_specific_25_hs.bed -b E096-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_kidney_specific_25_hs_lung_test.bed bedtools intersect -a human_chimp_kidney_specific_25_conserved.bed -b E096-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_kidney_specific_25_conserved_lung_test.bed
bedtools intersect -a human_chimp_rhesus_kidney_specific_25_hs.bed -b BI.Adult_Kidney.H3K27ac.27.broadPeak -wao -f 0.25 > human_chimp_rhesus_kidney_specific_25_hs_test.bed bedtools intersect -a human_chimp_rhesus_kidney_specific_25_conserved.bed -b BI.Adult_Kidney.H3K27ac.27.broadPeak -wao -f 0.25 > human_chimp_rhesus_kidney_specific_25_conserved_test.bed
bedtools intersect -a human_chimp_kidney_specific_50_hs.bed -b BI.Adult_Kidney.H3K27ac.27.broadPeak -wao -f 0.50 > human_chimp_kidney_specific_50_hs_test.bed bedtools intersect -a human_chimp_kidney_specific_50_conserved.bed -b BI.Adult_Kidney.H3K27ac.27.broadPeak -wao -f 0.50 > human_chimp_kidney_specific_50_conserved_test.bed bedtools intersect -a human_chimp_rhesus_kidney_specific_50_hs.bed -b BI.Adult_Kidney.H3K27ac.27.broadPeak -wao -f 0.50 > human_chimp_rhesus_kidney_specific_50_hs_test.bed bedtools intersect -a human_chimp_rhesus_kidney_specific_50_conserved.bed -b BI.Adult_Kidney.H3K27ac.27.broadPeak -wao -f 0.50 > human_chimp_rhesus_kidney_specific_50_conserved_test.bed
bedtools intersect -a human_chimp_kidney_specific_75_hs.bed -b BI.Adult_Kidney.H3K27ac.27.broadPeak -wao -f 0.75 > human_chimp_kidney_specific_75_hs_test.bed bedtools intersect -a human_chimp_kidney_specific_75_conserved.bed -b BI.Adult_Kidney.H3K27ac.27.broadPeak -wao -f 0.75 > human_chimp_kidney_specific_75_conserved_test.bed bedtools intersect -a human_chimp_rhesus_kidney_specific_75_hs.bed -b BI.Adult_Kidney.H3K27ac.27.broadPeak -wao -f 0.75 > human_chimp_rhesus_kidney_specific_75_hs_test.bed bedtools intersect -a human_chimp_rhesus_kidney_specific_75_conserved.bed -b BI.Adult_Kidney.H3K27ac.27.broadPeak -wao -f 0.75 > human_chimp_rhesus_kidney_specific_75_conserved_test.bed
bedtools intersect -a human_chimp_kidney_specific_25_hs.bed -b BI.Adult_Kidney.H3K27ac.153.broadPeak -wao -f 0.25 > human_chimp_kidney_specific_25_hs_test2.bed bedtools intersect -a human_chimp_kidney_specific_25_conserved.bed -b BI.Adult_Kidney.H3K27ac.153.broadPeak -wao -f 0.25 > human_chimp_kidney_specific_25_conserved_test2.bed bedtools intersect -a human_chimp_kidney_specific_25_hs.bed -b E096-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_kidney_specific_25_hs_lung_test2.bed bedtools intersect -a human_chimp_kidney_specific_25_conserved.bed -b E096-H3K27ac.broadPeak -wao -f 0.25 > human_chimp_kidney_specific_25_conserved_lung_test2.bed bedtools intersect -a human_chimp_rhesus_kidney_specific_25_hs.bed -b BI.Adult_Kidney.H3K27ac.153.broadPeak -wao -f 0.25 > human_chimp_rhesus_kidney_specific_25_hs_test2.bed bedtools intersect -a human_chimp_rhesus_kidney_specific_25_conserved.bed -b BI.Adult_Kidney.H3K27ac.153.broadPeak -wao -f 0.25 > human_chimp_rhesus_kidney_specific_25_conserved_test2.bed
bedtools intersect -a human_chimp_kidney_specific_50_hs.bed -b BI.Adult_Kidney.H3K27ac.153.broadPeak -wao -f 0.50 > human_chimp_kidney_specific_50_hs_test2.bed bedtools intersect -a human_chimp_kidney_specific_50_conserved.bed -b BI.Adult_Kidney.H3K27ac.153.broadPeak -wao -f 0.50 > human_chimp_kidney_specific_50_conserved_test2.bed bedtools intersect -a human_chimp_rhesus_kidney_specific_50_hs.bed -b BI.Adult_Kidney.H3K27ac.153.broadPeak -wao -f 0.50 > human_chimp_rhesus_kidney_specific_50_hs_test2.bed bedtools intersect -a human_chimp_rhesus_kidney_specific_50_conserved.bed -b BI.Adult_Kidney.H3K27ac.153.broadPeak -wao -f 0.50 > human_chimp_rhesus_kidney_specific_50_conserved_test2.bed
bedtools intersect -a human_chimp_kidney_specific_75_hs.bed -b BI.Adult_Kidney.H3K27ac.153.broadPeak -wao -f 0.75 > human_chimp_kidney_specific_75_hs_test2.bed bedtools intersect -a human_chimp_kidney_specific_75_conserved.bed -b BI.Adult_Kidney.H3K27ac.153.broadPeak -wao -f 0.75 > human_chimp_kidney_specific_75_conserved_test2.bed bedtools intersect -a human_chimp_rhesus_kidney_specific_75_hs.bed -b BI.Adult_Kidney.H3K27ac.153.broadPeak -wao -f 0.75 > human_chimp_rhesus_kidney_specific_75_hs_test2.bed bedtools intersect -a human_chimp_rhesus_kidney_specific_75_conserved.bed -b BI.Adult_Kidney.H3K27ac.153.broadPeak -wao -f 0.75 > human_chimp_rhesus_kidney_specific_75_conserved_test2.bed
bedtools intersect -a human_chimp_kidney_specific_25_hs.bed -b combined_kidney.bed -wao -f 0.25 > human_chimp_kidney_specific_25_hs_test3.bed bedtools intersect -a human_chimp_kidney_specific_25_conserved.bed -b combined_kidney.bed -wao -f 0.25 > human_chimp_kidney_specific_25_conserved_test3.bed bedtools intersect -a human_chimp_kidney_specific_50_hs.bed -b combined_kidney.bed -wao -f 0.50 > human_chimp_kidney_specific_50_hs_test3.bed bedtools intersect -a human_chimp_kidney_specific_50_conserved.bed -b combined_kidney.bed -wao -f 0.50 > human_chimp_kidney_specific_50_conserved_test3.bed bedtools intersect -a human_chimp_kidney_specific_75_hs.bed -b combined_kidney.bed -wao -f 0.75 > human_chimp_kidney_specific_75_hs_test3.bed bedtools intersect -a human_chimp_kidney_specific_75_conserved.bed -b combined_kidney.bed -wao -f 0.75 > human_chimp_kidney_specific_75_conserved_test3.bed
bedtools intersect -a human_chimp_heart_specific_25_hs.bed -b ENCSR501FWC_rep2_1_pe_bwa_biorep_filtered_hotspots.bed -wao -f 0.25 > human_chimp_heart_specific_25_hs_test.bed bedtools intersect -a human_chimp_heart_specific_25_conserved.bed -b ENCSR501FWC_rep2_1_pe_bwa_biorep_filtered_hotspots.bed -wao -f 0.25 > human_chimp_heart_specific_25_conserved_test.bed bedtools intersect -a human_chimp_heart_specific_50_hs.bed -b ENCSR501FWC_rep2_1_pe_bwa_biorep_filtered_hotspots.bed -wao -f 0.50 > human_chimp_heart_specific_50_hs_test.bed bedtools intersect -a human_chimp_heart_specific_50_conserved.bed -b ENCSR501FWC_rep2_1_pe_bwa_biorep_filtered_hotspots.bed -wao -f 0.50 > human_chimp_heart_specific_50_conserved_test.bed bedtools intersect -a human_chimp_heart_specific_75_hs.bed -b ENCSR501FWC_rep2_1_pe_bwa_biorep_filtered_hotspots.bed -wao -f 0.75 > human_chimp_heart_specific_75_hs_test.bed bedtools intersect -a human_chimp_heart_specific_75_conserved.bed -b ENCSR501FWC_rep2_1_pe_bwa_biorep_filtered_hotspots.bed -wao -f 0.75 > human_chimp_heart_specific_75_conserved_test.bed
bedtools intersect -a human_chimp_liver_specific_25_hs.bed -b ENCSR562FNN_rep1_1_pe_bwa_biorep_filtered_hotspots.bed -wao -f 0.25 > human_chimp_liver_specific_25_hs_test.bed bedtools intersect -a human_chimp_liver_specific_25_conserved.bed -b ENCSR562FNN_rep1_1_pe_bwa_biorep_filtered_hotspots.bed -wao -f 0.25 > human_chimp_liver_specific_25_conserved_test.bed bedtools intersect -a human_chimp_liver_specific_50_hs.bed -b ENCSR562FNN_rep1_1_pe_bwa_biorep_filtered_hotspots.bed -wao -f 0.50 > human_chimp_liver_specific_50_hs_test.bed bedtools intersect -a human_chimp_liver_specific_50_conserved.bed -b ENCSR562FNN_rep1_1_pe_bwa_biorep_filtered_hotspots.bed -wao -f 0.50 > human_chimp_liver_specific_50_conserved_test.bed bedtools intersect -a human_chimp_liver_specific_75_hs.bed -b ENCSR562FNN_rep1_1_pe_bwa_biorep_filtered_hotspots.bed -wao -f 0.75 > human_chimp_liver_specific_75_hs_test.bed bedtools intersect -a human_chimp_liver_specific_75_conserved.bed -b ENCSR562FNN_rep1_1_pe_bwa_biorep_filtered_hotspots.bed -wao -f 0.75 > human_chimp_liver_specific_75_conserved_test.bed
ENCSR541AVF_rep1_3_se_bwa_biorep_filtered_hotspots.bed
bedtools intersect -a human_chimp_lung_specific_25_hs.bed -b ENCSR541AVF_rep1_3_se_bwa_biorep_filtered_hotspots.bed -wao -f 0.25 > human_chimp_lung_specific_25_hs_test.bed bedtools intersect -a human_chimp_lung_specific_25_conserved.bed -b ENCSR541AVF_rep1_3_se_bwa_biorep_filtered_hotspots.bed -wao -f 0.25 > human_chimp_lung_specific_25_conserved_test.bed bedtools intersect -a human_chimp_lung_specific_50_hs.bed -b ENCSR541AVF_rep1_3_se_bwa_biorep_filtered_hotspots.bed -wao -f 0.50 > human_chimp_lung_specific_50_hs_test.bed bedtools intersect -a human_chimp_lung_specific_50_conserved.bed -b ENCSR541AVF_rep1_3_se_bwa_biorep_filtered_hotspots.bed -wao -f 0.50 > human_chimp_lung_specific_50_conserved_test.bed bedtools intersect -a human_chimp_lung_specific_75_hs.bed -b ENCSR541AVF_rep1_3_se_bwa_biorep_filtered_hotspots.bed -wao -f 0.75 > human_chimp_lung_specific_75_hs_test.bed bedtools intersect -a human_chimp_lung_specific_75_conserved.bed -b ENCSR541AVF_rep1_3_se_bwa_biorep_filtered_hotspots.bed -wao -f 0.75 > human_chimp_lung_specific_75_conserved_test.bed
ENCSR422PVL_rep1_2_se_bwa_biorep_filtered_hotspots.bed
bedtools intersect -a human_chimp_kidney_specific_25_hs.bed -b ENCSR422PVL_rep1_2_se_bwa_biorep_filtered_hotspots.bed -wao -f 0.25 > human_chimp_kidney_specific_25_hs_test2.bed bedtools intersect -a human_chimp_kidney_specific_25_conserved.bed -b ENCSR422PVL_rep1_2_se_bwa_biorep_filtered_hotspots.bed -wao -f 0.25 > human_chimp_kidney_specific_25_conserved_test2.bed bedtools intersect -a human_chimp_kidney_specific_50_hs.bed -b ENCSR422PVL_rep1_2_se_bwa_biorep_filtered_hotspots.bed -wao -f 0.50 > human_chimp_kidney_specific_50_hs_test2.bed bedtools intersect -a human_chimp_kidney_specific_50_conserved.bed -b ENCSR422PVL_rep1_2_se_bwa_biorep_filtered_hotspots.bed -wao -f 0.50 > human_chimp_kidney_specific_50_conserved_test2.bed bedtools intersect -a human_chimp_kidney_specific_75_hs.bed -b ENCSR422PVL_rep1_2_se_bwa_biorep_filtered_hotspots.bed -wao -f 0.75 > human_chimp_kidney_specific_75_hs_test2.bed bedtools intersect -a human_chimp_kidney_specific_75_conserved.bed -b ENCSR422PVL_rep1_2_se_bwa_biorep_filtered_hotspots.bed -wao -f 0.75 > human_chimp_kidney_specific_75_conserved_test2.bed
# Read in data- human specific
human_chimp_heart_specific_25_hs_test <- read.delim("../data/overlap_reg/human_chimp_heart_specific_25_hs_test.bed", header = FALSE)
dim(human_chimp_heart_specific_25_hs_test)## [1] 2591 14# Eliminate duplicates
dedup_human_chimp_heart_specific_25_hs_test <- human_chimp_heart_specific_25_hs_test[!duplicated(human_chimp_heart_specific_25_hs_test[,1:2]),]
dim(dedup_human_chimp_heart_specific_25_hs_test)## [1] 2509 14dedup_overlap_human_chimp_heart_specific_25_hs_test <- dedup_human_chimp_heart_specific_25_hs_test[which(dedup_human_chimp_heart_specific_25_hs_test$V6 != -1),]
# Look at fraction overlapping H3K27ac
location <- dedup_human_chimp_heart_specific_25_hs_test[which(dedup_human_chimp_heart_specific_25_hs_test$V6 != -1),]
nrow(location)/nrow(human_chimp_heart_specific_25_hs_test)## [1] 0.5773832# Read in data- human and chimp conserved
human_chimp_heart_specific_25_conserved_test <- read.delim("../data/overlap_reg/human_chimp_heart_specific_25_conserved_test.bed", header = FALSE)
dedup_overlap_human_chimp_heart_specific_25_conserved_test <- human_chimp_heart_specific_25_conserved_test[which(human_chimp_heart_specific_25_conserved_test$V6 != -1),]
nrow(dedup_overlap_human_chimp_heart_specific_25_conserved_test)/nrow(human_chimp_heart_specific_25_conserved_test)## [1] 0.6534447# Run a difference in proportions test
res <- prop.test(x = c(1918, 373), n = c(2473, 441))
res##
## 2-sample test for equality of proportions with continuity
## correction
##
## data: c(1918, 373) out of c(2473, 441)
## X-squared = 10.568, df = 1, p-value = 0.001151
## alternative hypothesis: two.sided
## 95 percent confidence interval:
## -0.10906708 -0.03139045
## sample estimates:
## prop 1 prop 2
## 0.7755762 0.8458050# What if we look at just the hypermethylated regions
# Human Specific
hyper_only_hs <- human_chimp_heart_specific_25_hs_test[which(human_chimp_heart_specific_25_hs_test[,4] == "hyper"),]
hyper_only_hs_overlap <- hyper_only_hs[which(hyper_only_hs$V6 != -1),]
nrow(hyper_only_hs_overlap)/nrow(hyper_only_hs)## [1] 0.2222222# Conserved
hyper_only_conserved <- human_chimp_heart_specific_25_conserved_test[which(human_chimp_heart_specific_25_conserved_test[,4] == "hyper"),]
hyper_only_conserved_overlap <- hyper_only_conserved[which(hyper_only_conserved$V6 != -1),]
nrow(hyper_only_conserved_overlap)/nrow(hyper_only_conserved)## [1] 0.1627907# What if we look at just the hypomethylated regions (hypomethylated regions, aka regions of less methylation, are more likely to be associated with an activating mark like H3K27ac)
# Human Specific
hyper_only_hs <- human_chimp_heart_specific_25_hs_test[which(human_chimp_heart_specific_25_hs_test[,4] == "hypo"),]
hyper_only_hs_overlap <- hyper_only_hs[which(hyper_only_hs$V6 != -1),]
nrow(hyper_only_hs_overlap)/nrow(hyper_only_hs)## [1] 0.6660762# Conserved
hyper_only_conserved <- human_chimp_heart_specific_25_conserved_test[which(human_chimp_heart_specific_25_conserved_test[,4] == "hypo"),]
hyper_only_conserved_overlap <- hyper_only_conserved[which(hyper_only_conserved$V6 != -1),]
nrow(hyper_only_conserved_overlap)/nrow(hyper_only_conserved)## [1] 0.7018349# Run the t test
res <- prop.test(x = c(nrow(hyper_only_hs_overlap), nrow(hyper_only_conserved_overlap)), n = c(nrow(hyper_only_hs), nrow(hyper_only_conserved)))
res##
## 2-sample test for equality of proportions with continuity
## correction
##
## data: c(nrow(hyper_only_hs_overlap), nrow(hyper_only_conserved_overlap)) out of c(nrow(hyper_only_hs), nrow(hyper_only_conserved))
## X-squared = 1.9604, df = 1, p-value = 0.1615
## alternative hypothesis: two.sided
## 95 percent confidence interval:
## -0.08426650 0.01274913
## sample estimates:
## prop 1 prop 2
## 0.6660762 0.7018349# Make a function that exports fraction overlap and p values of the differences for all data (row 1), hypomethylated data (row 2; what we are arguably most interested in), and hypermethylated data (row 3)
diff_prop_hs_versus_conserved <- function(filename_human_specific, filename_conserved){
######################################### FIRST, RUN THE FUNCTION ON ALL DATA #####################
# Start with the human specific data
filename_human_specific_overlap <- filename_human_specific[which(filename_human_specific$V6 != -1),]
# Look at fraction overlapping H3K27ac
fraction_hs_overlap <- nrow(filename_human_specific_overlap)/nrow(filename_human_specific)
# Then, the conserved data
filename_conserved_overlap <- filename_conserved[which(filename_conserved$V6 != -1),]
fraction_conserved_overlap <- nrow(filename_conserved_overlap)/nrow(filename_conserved)
# Run a difference in proportions test
res <- prop.test(x = c(nrow(filename_human_specific_overlap), nrow(filename_conserved_overlap)), n = c(nrow(filename_human_specific), nrow(filename_conserved)))
import_values_1 <- cbind(fraction_hs_overlap, fraction_conserved_overlap, res$p.value)
######################################### NEXT, RUN THE FUNCTION ON HYPOMETHYLATED DATA #####################
# Human Specific
hypo_only_hs <- filename_human_specific[which(filename_human_specific[,4] == "hypo"),]
hypo_only_hs_overlap <- hypo_only_hs[which(hypo_only_hs$V6 != -1),]
fraction_hypo_hs_overlap <- nrow(hypo_only_hs_overlap)/nrow(hypo_only_hs)
# Conserved
hypo_only_conserved <- filename_conserved[which(filename_conserved[,4] == "hypo"),]
hypo_only_conserved_overlap <- hypo_only_conserved[which(hypo_only_conserved$V6 != -1),]
fraction_hypo_conserved_overlap <- nrow(hypo_only_conserved_overlap)/nrow(hypo_only_conserved)
# Run a difference in proportions test
res <- prop.test(x = c(nrow(hypo_only_hs_overlap), nrow(hypo_only_conserved_overlap)), n = c(nrow(hypo_only_hs), nrow(hypo_only_conserved)))
import_values_2 <- cbind(fraction_hypo_hs_overlap, fraction_hypo_conserved_overlap, res$p.value)
######################################### NEXT, RUN THE FUNCTION ON HYPERMETHYLATED DATA #####################
# Human Specific
hypo_only_hs <- filename_human_specific[which(filename_human_specific[,4] == "hyper"),]
hypo_only_hs_overlap <- hypo_only_hs[which(hypo_only_hs$V6 != -1),]
fraction_hypo_hs_overlap <- nrow(hypo_only_hs_overlap)/nrow(hypo_only_hs)
# Conserved
hypo_only_conserved <- filename_conserved[which(filename_conserved[,4] == "hyper"),]
hypo_only_conserved_overlap <- hypo_only_conserved[which(hypo_only_conserved$V6 != -1),]
fraction_hypo_conserved_overlap <- nrow(hypo_only_conserved_overlap)/nrow(hypo_only_conserved)
# Run a difference in proportions test
res <- prop.test(x = c(nrow(hypo_only_hs_overlap), nrow(hypo_only_conserved_overlap)), n = c(nrow(hypo_only_hs), nrow(hypo_only_conserved)))
import_values_3 <- cbind(fraction_hypo_hs_overlap, fraction_hypo_conserved_overlap, res$p.value)
import_values <- rbind(import_values_1, import_values_2, import_values_3)
return(import_values)
}
#diff_prop_hs_versus_conserved(human_chimp_heart_specific_25_hs_test, human_chimp_heart_specific_25_conserved_test)
# Run with liver to compare
#human_chimp_heart_specific_25_hs_test_liver <- read.delim("../data/overlap_reg/human_chimp_heart_specific_25_hs_liver_test.bed", header = FALSE)
#human_chimp_heart_specific_25_conserved_test_liver <- read.delim("../data/overlap_reg/human_chimp_heart_specific_25_conserved_liver_test.bed", header = FALSE)
#diff_prop_hs_versus_conserved(human_chimp_heart_specific_25_hs_test_liver, human_chimp_heart_specific_25_conserved_test_liver)# Heart specific 25%- human and chimp
human_chimp_heart_specific_25_hs_test <- read.delim("../data/overlap_reg/human_chimp_heart_specific_25_hs_test.bed", header = FALSE)
human_chimp_heart_specific_25_conserved_test <- read.delim("../data/overlap_reg/human_chimp_heart_specific_25_conserved_test.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_heart_specific_25_hs_test, human_chimp_heart_specific_25_conserved_test)## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.6090313 0.6534447 0.07427587
## [2,] 0.6660762 0.7018349 0.16146641
## [3,] 0.2222222 0.1627907 0.48704248# Heart specific 25%- human, chimp, and rhesus
human_chimp_rhesus_heart_specific_25_hs_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_heart_specific_25_hs_test.bed", header = FALSE)
human_chimp_rhesus_heart_specific_25_conserved_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_heart_specific_25_conserved_test.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_rhesus_heart_specific_25_hs_test, human_chimp_rhesus_heart_specific_25_conserved_test)## Warning in prop.test(x = c(nrow(hypo_only_hs_overlap),
## nrow(hypo_only_conserved_overlap)), : Chi-squared approximation may be
## incorrect## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.7756118 0.8550725 0.1559953
## [2,] 0.8094556 0.8923077 0.1279157
## [3,] 0.5520505 0.2500000 0.4834394# Heart specific 50%- human and chimp
human_chimp_heart_specific_50_hs_test <- read.delim("../data/overlap_reg/human_chimp_heart_specific_50_hs_test.bed", header = FALSE)
human_chimp_heart_specific_50_conserved_test <- read.delim("../data/overlap_reg/human_chimp_heart_specific_50_conserved_test.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_heart_specific_50_hs_test, human_chimp_heart_specific_50_conserved_test)## Warning in prop.test(x = c(nrow(hypo_only_hs_overlap),
## nrow(hypo_only_conserved_overlap)), : Chi-squared approximation may be
## incorrect## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.4263607 0.4324324 0.9059476
## [2,] 0.4634731 0.4567901 0.8994426
## [3,] 0.1225490 0.0625000 0.7532367# Heart specific 50%- human, chimp, and rhesus
human_chimp_rhesus_heart_specific_50_hs_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_heart_specific_50_hs_test.bed", header = FALSE)
human_chimp_rhesus_heart_specific_50_conserved_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_heart_specific_50_conserved_test.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_rhesus_heart_specific_50_hs_test, human_chimp_rhesus_heart_specific_50_conserved_test)## Warning in prop.test(x = c(nrow(hypo_only_hs_overlap),
## nrow(hypo_only_conserved_overlap)), : Chi-squared approximation may be
## incorrect## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.7424492 0.9024390 0.03188221
## [2,] 0.7725031 0.9473684 0.01823557
## [3,] 0.4974874 0.3333333 1.00000000# Heart specific 75%- human and chimp
human_chimp_heart_specific_75_hs_test <- read.delim("../data/overlap_reg/human_chimp_heart_specific_75_hs_test.bed", header = FALSE)
human_chimp_heart_specific_75_conserved_test <- read.delim("../data/overlap_reg/human_chimp_heart_specific_75_conserved_test.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_heart_specific_75_hs_test, human_chimp_heart_specific_75_conserved_test)## Warning in prop.test(x = c(nrow(hypo_only_hs_overlap),
## nrow(hypo_only_conserved_overlap)), : Chi-squared approximation may be
## incorrect## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.2903907 0.2608696 0.7911581
## [2,] 0.3058419 0.2727273 0.7657660
## [3,] 0.1081081 0.0000000 1.0000000# Heart specific 75%- human, chimp, and rhesus
human_chimp_rhesus_heart_specific_75_hs_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_heart_specific_75_hs_test.bed", header = FALSE)
human_chimp_rhesus_heart_specific_75_conserved_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_heart_specific_75_conserved_test.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_rhesus_heart_specific_75_hs_test, human_chimp_rhesus_heart_specific_75_conserved_test)## Warning in prop.test(x = c(nrow(filename_human_specific_overlap),
## nrow(filename_conserved_overlap)), : Chi-squared approximation may be
## incorrect
## Warning in prop.test(x = c(nrow(filename_human_specific_overlap),
## nrow(filename_conserved_overlap)), : Chi-squared approximation may be
## incorrect
## Warning in prop.test(x = c(nrow(filename_human_specific_overlap),
## nrow(filename_conserved_overlap)), : Chi-squared approximation may be
## incorrect## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.7124464 0.6666667 1.0000000
## [2,] 0.7299185 1.0000000 0.9504976
## [3,] 0.5068493 0.0000000 1.0000000Row 2 is the hypomethylated region.
# Liver specific 25%- human and chimp
human_chimp_heart_specific_25_hs_test <- read.delim("../data/overlap_reg/human_chimp_liver_specific_25_hs_test.bed", header = FALSE)
human_chimp_heart_specific_25_conserved_test <- read.delim("../data/overlap_reg/human_chimp_liver_specific_25_conserved_test.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_heart_specific_25_hs_test, human_chimp_heart_specific_25_conserved_test)## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.2675483 0.3071799 0.0143412074
## [2,] 0.2183250 0.2790485 0.0005617279
## [3,] 0.3884007 0.4263566 0.3392974626# liver specific 25%- human, chimp, and rhesus
#human_chimp_rhesus_heart_specific_25_hs_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_liver_specific_25_hs_test.bed", header = FALSE)
#human_chimp_rhesus_heart_specific_25_conserved_test <- read.table("../data/overlap_reg/human_chimp_rhesus_liver_specific_25_conserved_test.bed", header = FALSE)
#diff_prop_hs_versus_conserved(human_chimp_rhesus_heart_specific_25_hs_test, human_chimp_rhesus_heart_specific_25_conserved_test)
# liver specific 50%- human and chimp
human_chimp_heart_specific_50_hs_test <- read.delim("../data/overlap_reg/human_chimp_liver_specific_50_hs_test.bed", header = FALSE)
human_chimp_heart_specific_50_conserved_test <- read.delim("../data/overlap_reg/human_chimp_liver_specific_50_conserved_test.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_heart_specific_50_hs_test, human_chimp_heart_specific_50_conserved_test)## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.1646377 0.1606218 0.8475217
## [2,] 0.1203704 0.1386749 0.2833358
## [3,] 0.2983683 0.2764228 0.7196738# liver specific 50%- human, chimp, and rhesus
#human_chimp_rhesus_heart_specific_50_hs_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_liver_specific_50_hs_test.bed", header = FALSE)
#human_chimp_rhesus_heart_specific_50_conserved_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_liver_specific_50_conserved_test.bed", header = FALSE)
#diff_prop_hs_versus_conserved(human_chimp_rhesus_heart_specific_50_hs_test, human_chimp_rhesus_heart_specific_50_conserved_test)
# liver specific 75%- human and chimp
human_chimp_heart_specific_75_hs_test <- read.delim("../data/overlap_reg/human_chimp_liver_specific_75_hs_test.bed", header = FALSE)
human_chimp_heart_specific_75_conserved_test <- read.delim("../data/overlap_reg/human_chimp_liver_specific_75_conserved_test.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_heart_specific_75_hs_test, human_chimp_heart_specific_75_conserved_test)## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.08370837 0.09905660 0.5510101
## [2,] 0.06394708 0.08839779 0.3024212
## [3,] 0.17156863 0.16129032 1.0000000# liver specific 75%- human, chimp, and rhesus
#human_chimp_rhesus_heart_specific_75_hs_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_liver_specific_75_hs_test.bed", header = FALSE)
#human_chimp_rhesus_heart_specific_75_conserved_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_liver_specific_75_conserved_test.bed", header = FALSE)
#diff_prop_hs_versus_conserved(human_chimp_rhesus_heart_specific_75_hs_test, human_chimp_rhesus_heart_specific_75_conserved_test)# lung specific 25%- human and chimp
human_chimp_heart_specific_25_hs_test <- read.delim("../data/overlap_reg/human_chimp_lung_specific_25_hs_test.bed", header = FALSE)
human_chimp_heart_specific_25_conserved_test <- read.delim("../data/overlap_reg/human_chimp_lung_specific_25_conserved_test.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_heart_specific_25_hs_test, human_chimp_heart_specific_25_conserved_test)## Warning in prop.test(x = c(nrow(hypo_only_hs_overlap),
## nrow(hypo_only_conserved_overlap)), : Chi-squared approximation may be
## incorrect
## Warning in prop.test(x = c(nrow(hypo_only_hs_overlap),
## nrow(hypo_only_conserved_overlap)), : Chi-squared approximation may be
## incorrect## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.12149533 0.1568627 0.6188327
## [2,] 0.16783217 0.1428571 1.0000000
## [3,] 0.09824561 0.1666667 0.3949900# lung specific 25%- human, chimp, and rhesus
#human_chimp_rhesus_heart_specific_25_hs_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_lung_specific_25_hs_test.bed", header = FALSE)
#human_chimp_rhesus_heart_specific_25_conserved_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_lung_specific_25_conserved_test.bed", header = FALSE)
#diff_prop_hs_versus_conserved(human_chimp_rhesus_heart_specific_25_hs_test, human_chimp_rhesus_heart_specific_25_conserved_test)
# lung specific 50%- human and chimp
human_chimp_heart_specific_50_hs_test <- read.delim("../data/overlap_reg/human_chimp_lung_specific_50_hs_test.bed", header = FALSE)
human_chimp_heart_specific_50_conserved_test <- read.delim("../data/overlap_reg/human_chimp_lung_specific_50_conserved_test.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_heart_specific_50_hs_test, human_chimp_heart_specific_50_conserved_test)## Warning in prop.test(x = c(nrow(filename_human_specific_overlap),
## nrow(filename_conserved_overlap)), : Chi-squared approximation may be
## incorrect
## Warning in prop.test(x = c(nrow(filename_human_specific_overlap),
## nrow(filename_conserved_overlap)), : Chi-squared approximation may be
## incorrect
## Warning in prop.test(x = c(nrow(filename_human_specific_overlap),
## nrow(filename_conserved_overlap)), : Chi-squared approximation may be
## incorrect## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.08230453 0.1304348 0.6914651
## [2,] 0.09722222 0.1250000 1.0000000
## [3,] 0.07602339 0.1333333 0.7740207# lung specific 50%- human, chimp, and rhesus
#human_chimp_rhesus_heart_specific_50_hs_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_lung_specific_50_hs_test.bed", header = FALSE)
#human_chimp_rhesus_heart_specific_50_conserved_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_lung_specific_50_conserved_test.bed", header = FALSE)
#diff_prop_hs_versus_conserved(human_chimp_rhesus_heart_specific_50_hs_test, human_chimp_rhesus_heart_specific_50_conserved_test)
# lung specific 75%- human and chimp
#human_chimp_heart_specific_75_hs_test <- read.delim("../data/overlap_reg/human_chimp_lung_specific_75_hs_test.bed", header = FALSE)
#human_chimp_heart_specific_75_conserved_test <- read.delim("../data/overlap_reg/human_chimp_lung_specific_75_conserved_test.bed", header = FALSE)
#diff_prop_hs_versus_conserved(human_chimp_heart_specific_75_hs_test, human_chimp_heart_specific_75_conserved_test)
# lung specific 75%- human, chimp, and rhesus
#human_chimp_rhesus_heart_specific_75_hs_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_lung_specific_75_hs_test.bed", header = FALSE)
#human_chimp_rhesus_heart_specific_75_conserved_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_lung_specific_75_conserved_test.bed", header = FALSE)
#diff_prop_hs_versus_conserved(human_chimp_rhesus_heart_specific_75_hs_test, human_chimp_rhesus_heart_specific_75_conserved_test)# kidney specific 25%- human and chimp
human_chimp_heart_specific_25_hs_test <- read.delim("../data/overlap_reg/human_chimp_kidney_specific_25_hs_test.bed", header = FALSE)
human_chimp_heart_specific_25_conserved_test <- read.delim("../data/overlap_reg/human_chimp_kidney_specific_25_conserved_test.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_heart_specific_25_hs_test, human_chimp_heart_specific_25_conserved_test)## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.6044386 0.6265329 0.2484979
## [2,] 0.5645161 0.6666667 0.3185271
## [3,] 0.6070188 0.6247086 0.3718584# kidney specific 25%- human, chimp, and rhesus
human_chimp_rhesus_heart_specific_25_hs_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_kidney_specific_25_hs_test.bed", header = FALSE)
human_chimp_rhesus_heart_specific_25_conserved_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_kidney_specific_25_conserved_test.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_rhesus_heart_specific_25_hs_test, human_chimp_rhesus_heart_specific_25_conserved_test)## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.6119726 0.5719064 0.1984457
## [2,] 0.5454545 0.5000000 0.9317478
## [3,] 0.6161810 0.5759717 0.2097119# kidney specific 50%- human and chimp
human_chimp_heart_specific_50_hs_test <- read.delim("../data/overlap_reg/human_chimp_kidney_specific_50_hs_test.bed", header = FALSE)
human_chimp_heart_specific_50_conserved_test <- read.delim("../data/overlap_reg/human_chimp_kidney_specific_50_conserved_test.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_heart_specific_50_hs_test, human_chimp_heart_specific_50_conserved_test)## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.5590615 0.5798165 0.4028833
## [2,] 0.5433071 0.6785714 0.2725937
## [3,] 0.5599147 0.5744681 0.5790053# kidney specific 50%- human, chimp, and rhesus
human_chimp_rhesus_heart_specific_50_hs_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_kidney_specific_50_hs_test.bed", header = FALSE)
human_chimp_rhesus_heart_specific_50_conserved_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_kidney_specific_50_conserved_test.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_rhesus_heart_specific_50_hs_test, human_chimp_rhesus_heart_specific_50_conserved_test)## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.5607723 0.4397163 0.006550611
## [2,] 0.5294118 0.5454545 1.000000000
## [3,] 0.5625000 0.4307692 0.004449768# kidney specific 75%- human and chimp
human_chimp_heart_specific_75_hs_test <- read.delim("../data/overlap_reg/human_chimp_kidney_specific_75_hs_test.bed", header = FALSE)
human_chimp_heart_specific_75_conserved_test <- read.delim("../data/overlap_reg/human_chimp_kidney_specific_75_conserved_test.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_heart_specific_75_hs_test, human_chimp_heart_specific_75_conserved_test)## Warning in prop.test(x = c(nrow(hypo_only_hs_overlap),
## nrow(hypo_only_conserved_overlap)), : Chi-squared approximation may be
## incorrect## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.5079251 0.4545455 0.2594192
## [2,] 0.4285714 0.4545455 1.0000000
## [3,] 0.5112613 0.4545455 0.2493508# kdiney specific 75%- human, chimp, and rhesus
human_chimp_rhesus_heart_specific_75_hs_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_kidney_specific_75_hs_test.bed", header = FALSE)
human_chimp_rhesus_heart_specific_75_conserved_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_kidney_specific_75_conserved_test.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_rhesus_heart_specific_75_hs_test, human_chimp_rhesus_heart_specific_75_conserved_test)## Warning in prop.test(x = c(nrow(hypo_only_hs_overlap),
## nrow(hypo_only_conserved_overlap)), : Chi-squared approximation may be
## incorrect## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.5137957 0.2105263 0.0166335
## [2,] 0.4181818 0.0000000 1.0000000
## [3,] 0.5178849 0.2222222 0.0241384# kidney specific 25%- human and chimp
human_chimp_heart_specific_25_hs_test <- read.delim("../data/overlap_reg/human_chimp_kidney_specific_25_hs_test2.bed", header = FALSE)
human_chimp_heart_specific_25_conserved_test <- read.delim("../data/overlap_reg/human_chimp_kidney_specific_25_conserved_test2.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_heart_specific_25_hs_test, human_chimp_heart_specific_25_conserved_test)## Warning in prop.test(x = c(nrow(hypo_only_hs_overlap),
## nrow(hypo_only_conserved_overlap)), : Chi-squared approximation may be
## incorrect## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.05014653 0.07461024 0.006343597
## [2,] 0.00000000 0.00000000 NaN
## [3,] 0.05337955 0.07799767 0.009187823# kidney specific 25%- human, chimp, and rhesus
human_chimp_rhesus_heart_specific_25_hs_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_kidney_specific_25_hs_test2.bed", header = FALSE)
human_chimp_rhesus_heart_specific_25_conserved_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_kidney_specific_25_conserved_test2.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_rhesus_heart_specific_25_hs_test, human_chimp_rhesus_heart_specific_25_conserved_test)## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.7100613 0.6822742 0.3490362
## [2,] 0.6666667 0.6250000 0.9524119
## [3,] 0.7128067 0.6855124 0.3722546# kidney specific 50%- human and chimp
human_chimp_heart_specific_50_hs_test <- read.delim("../data/overlap_reg/human_chimp_kidney_specific_50_hs_test2.bed", header = FALSE)
human_chimp_heart_specific_50_conserved_test <- read.delim("../data/overlap_reg/human_chimp_kidney_specific_50_conserved_test2.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_heart_specific_50_hs_test, human_chimp_heart_specific_50_conserved_test)## Warning in prop.test(x = c(nrow(hypo_only_hs_overlap),
## nrow(hypo_only_conserved_overlap)), : Chi-squared approximation may be
## incorrect## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.01941748 0.02201835 0.8226097
## [2,] 0.00000000 0.00000000 NaN
## [3,] 0.02046908 0.02321083 0.8225119# kidney specific 50%- human, chimp, and rhesus
human_chimp_rhesus_heart_specific_50_hs_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_kidney_specific_50_hs_test2.bed", header = FALSE)
human_chimp_rhesus_heart_specific_50_conserved_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_kidney_specific_50_conserved_test2.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_rhesus_heart_specific_50_hs_test, human_chimp_rhesus_heart_specific_50_conserved_test)## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.6458973 0.5673759 0.07247934
## [2,] 0.5294118 0.6363636 0.71533366
## [3,] 0.6523148 0.5615385 0.04452769# kidney specific 75%- human and chimp
human_chimp_heart_specific_75_hs_test <- read.delim("../data/overlap_reg/human_chimp_kidney_specific_75_hs_test2.bed", header = FALSE)
human_chimp_heart_specific_75_conserved_test <- read.delim("../data/overlap_reg/human_chimp_kidney_specific_75_conserved_test2.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_heart_specific_75_hs_test, human_chimp_heart_specific_75_conserved_test)## Warning in prop.test(x = c(nrow(filename_human_specific_overlap),
## nrow(filename_conserved_overlap)), : Chi-squared approximation may be
## incorrect
## Warning in prop.test(x = c(nrow(filename_human_specific_overlap),
## nrow(filename_conserved_overlap)), : Chi-squared approximation may be
## incorrect
## Warning in prop.test(x = c(nrow(filename_human_specific_overlap),
## nrow(filename_conserved_overlap)), : Chi-squared approximation may be
## incorrect## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.005043228 0.02097902 0.08775972
## [2,] 0.000000000 0.00000000 NaN
## [3,] 0.005255255 0.02272727 0.07659695# kdiney specific 75%- human, chimp, and rhesus
human_chimp_rhesus_heart_specific_75_hs_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_kidney_specific_75_hs_test2.bed", header = FALSE)
human_chimp_rhesus_heart_specific_75_conserved_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_kidney_specific_75_conserved_test2.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_rhesus_heart_specific_75_hs_test, human_chimp_rhesus_heart_specific_75_conserved_test)## Warning in prop.test(x = c(nrow(hypo_only_hs_overlap),
## nrow(hypo_only_conserved_overlap)), : Chi-squared approximation may be
## incorrect## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.5704698 0.3157895 0.04641865
## [2,] 0.4727273 0.0000000 1.00000000
## [3,] 0.5746501 0.3333333 0.06957496# kidney specific 25%- human and chimp
human_chimp_heart_specific_25_hs_test <- read.delim("../data/overlap_reg/human_chimp_kidney_specific_25_hs_test3.bed", header = FALSE)
human_chimp_heart_specific_25_conserved_test <- read.delim("../data/overlap_reg/human_chimp_kidney_specific_25_conserved_test3.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_heart_specific_25_hs_test, human_chimp_heart_specific_25_conserved_test)## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.3730418 0.3857302 0.5151373
## [2,] 0.2903226 0.3846154 0.3319795
## [3,] 0.3783878 0.3857809 0.7252123# kidney specific 50%- human and chimp
human_chimp_heart_specific_50_hs_test <- read.delim("../data/overlap_reg/human_chimp_kidney_specific_50_hs_test3.bed", header = FALSE)
human_chimp_heart_specific_50_conserved_test <- read.delim("../data/overlap_reg/human_chimp_kidney_specific_50_conserved_test3.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_heart_specific_50_hs_test, human_chimp_heart_specific_50_conserved_test)## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.3559871 0.3688073 0.60610114
## [2,] 0.2440945 0.4642857 0.03506309
## [3,] 0.3620469 0.3636364 0.98602355# kidney specific 75%- human and chimp
human_chimp_heart_specific_75_hs_test <- read.delim("../data/overlap_reg/human_chimp_kidney_specific_75_hs_test3.bed", header = FALSE)
human_chimp_heart_specific_75_conserved_test <- read.delim("../data/overlap_reg/human_chimp_kidney_specific_75_conserved_test3.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_heart_specific_75_hs_test, human_chimp_heart_specific_75_conserved_test)## Warning in prop.test(x = c(nrow(hypo_only_hs_overlap),
## nrow(hypo_only_conserved_overlap)), : Chi-squared approximation may be
## incorrect## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.3386167 0.3076923 0.5140024
## [2,] 0.2500000 0.3636364 0.6852371
## [3,] 0.3423423 0.3030303 0.4157341# kdiney specific 75%- human, chimp, and rhesus
human_chimp_rhesus_heart_specific_75_hs_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_kidney_specific_75_hs_test2.bed", header = FALSE)
human_chimp_rhesus_heart_specific_75_conserved_test <- read.delim("../data/overlap_reg/human_chimp_rhesus_kidney_specific_75_conserved_test2.bed", header = FALSE)
diff_prop_hs_versus_conserved(human_chimp_rhesus_heart_specific_75_hs_test, human_chimp_rhesus_heart_specific_75_conserved_test)## Warning in prop.test(x = c(nrow(hypo_only_hs_overlap),
## nrow(hypo_only_conserved_overlap)), : Chi-squared approximation may be
## incorrect## fraction_hs_overlap fraction_conserved_overlap
## [1,] 0.5704698 0.3157895 0.04641865
## [2,] 0.4727273 0.0000000 1.00000000
## [3,] 0.5746501 0.3333333 0.06957496