Looking at number of genes per tissue
cpm_12184 <- read.delim("~/Desktop/Reg_Evo_Primates/data/cpm_12184.txt")
chimp_heart <- c(1, 5, 9, 13)
human_heart <- c(20, 24, 28)
rhesus_heart <- c(32, 36, 40, 44)
chimp_kidney <- c(2, 6, 10, 14)
human_kidney <- c(17, 21, 25, 29)
rhesus_kidney <- c(33, 37, 41, 45)
chimp_liver <- c(3, 7, 11, 15)
human_liver <- c(18, 22, 26, 30)
rhesus_liver <- c(34, 38, 42, 46)
chimp_lung <- c(4, 8, 12, 16)
human_lung <- c(19, 23, 27, 31)
rhesus_lung <- c(35, 39, 43, 47)
# Expression on a per tissue, per species basis
chimp_heart_exp <- cpm_12184[,chimp_heart]
human_heart_exp <- cpm_12184[,human_heart]
rhesus_heart_exp <- cpm_12184[,rhesus_heart]
chimp_kidney_exp <- cpm_12184[,chimp_kidney]
human_kidney_exp <- cpm_12184[,human_kidney]
summary(apply(human_kidney_exp, 1, mean) > 1.5)
## Mode FALSE TRUE
## logical 489 11695
summary(rowSums(human_kidney_exp > 1.5) >= 2)
## Mode FALSE TRUE
## logical 364 11820
rhesus_kidney_exp <- cpm_12184[,rhesus_kidney]
summary(apply(rhesus_kidney_exp, 1, mean) > 1.5)
## Mode FALSE TRUE
## logical 769 11415
summary(rowSums(rhesus_kidney_exp > 1.5) >= 2)
## Mode FALSE TRUE
## logical 669 11515
chimp_liver_exp <- cpm_12184[,chimp_liver]
summary(apply(chimp_liver_exp, 1, mean) > 1.5)
## Mode FALSE TRUE
## logical 920 11264
summary(rowSums(chimp_liver_exp > 1.5) >= 2)
## Mode FALSE TRUE
## logical 735 11449
human_liver_exp <- cpm_12184[,human_liver]
summary(apply(human_liver_exp, 1, mean) > 1.5)
## Mode FALSE TRUE
## logical 745 11439
summary(rowSums(human_liver_exp > 1.5) >= 2)
## Mode FALSE TRUE
## logical 568 11616
rhesus_liver_exp <- cpm_12184[,rhesus_liver]
summary(apply(rhesus_liver_exp, 1, mean) > 1.5)
## Mode FALSE TRUE
## logical 1202 10982
summary(rowSums(rhesus_liver_exp > 1.5) >= 2)
## Mode FALSE TRUE
## logical 1099 11085
chimp_lung_exp <- cpm_12184[,chimp_lung]
summary(apply(chimp_lung_exp, 1, mean) > 1.5)
## Mode FALSE TRUE
## logical 599 11585
summary(rowSums(chimp_lung_exp > 1.5) >= 2)
## Mode FALSE TRUE
## logical 465 11719
human_lung_exp <- cpm_12184[,human_lung]
summary(apply(human_lung_exp, 1, mean) > 1.5)
## Mode FALSE TRUE
## logical 480 11704
summary(rowSums(human_lung_exp > 1.5) >= 2)
## Mode FALSE TRUE
## logical 384 11800
rhesus_lung_exp <- cpm_12184[,rhesus_lung]
summary(apply(rhesus_lung_exp, 1, mean) > 1.5)
## Mode FALSE TRUE
## logical 674 11510
summary(rowSums(rhesus_lung_exp > 1.5) >= 2)
## Mode FALSE TRUE
## logical 604 11580
summary(apply(chimp_heart_exp, 1, mean) > 1.5)
## Mode FALSE TRUE
## logical 804 11380
summary(apply(human_heart_exp, 1, mean) > 1.5)
## Mode FALSE TRUE
## logical 865 11319
summary(apply(rhesus_heart_exp, 1, mean) > 1.5)
## Mode FALSE TRUE
## logical 1096 11088
summary(apply(chimp_kidney_exp, 1, mean) > 1.5)
## Mode FALSE TRUE
## logical 475 11709
summary(apply(human_kidney_exp, 1, mean) > 1.5)
## Mode FALSE TRUE
## logical 489 11695
summary(apply(rhesus_kidney_exp, 1, mean) > 1.5)
## Mode FALSE TRUE
## logical 769 11415
summary(apply(chimp_liver_exp, 1, mean) > 1.5)
## Mode FALSE TRUE
## logical 920 11264
summary(apply(human_liver_exp, 1, mean) > 1.5)
## Mode FALSE TRUE
## logical 745 11439
summary(apply(rhesus_liver_exp, 1, mean) > 1.5)
## Mode FALSE TRUE
## logical 1202 10982
summary(apply(chimp_lung_exp, 1, mean) > 1.5)
## Mode FALSE TRUE
## logical 599 11585
summary(apply(human_lung_exp, 1, mean) > 1.5)
## Mode FALSE TRUE
## logical 480 11704
summary(apply(rhesus_lung_exp, 1, mean) > 1.5)
## Mode FALSE TRUE
## logical 674 11510
summary(rowSums(chimp_heart_exp > 1.5) >= 2)
## Mode FALSE TRUE
## logical 665 11519
summary(rowSums(human_heart_exp > 1.5) >= 2)
## Mode FALSE TRUE
## logical 824 11360
summary(rowSums(rhesus_heart_exp > 1.5) >= 2)
## Mode FALSE TRUE
## logical 983 11201
summary(rowSums(chimp_kidney_exp > 1.5) >= 2)
## Mode FALSE TRUE
## logical 370 11814
summary(rowSums(human_kidney_exp > 1.5) >= 2)
## Mode FALSE TRUE
## logical 364 11820
summary(rowSums(rhesus_kidney_exp > 1.5) >= 2)
## Mode FALSE TRUE
## logical 669 11515
summary(rowSums(chimp_liver_exp > 1.5) >= 2)
## Mode FALSE TRUE
## logical 735 11449
summary(rowSums(human_liver_exp > 1.5) >= 2)
## Mode FALSE TRUE
## logical 568 11616
summary(rowSums(rhesus_liver_exp > 1.5) >= 2)
## Mode FALSE TRUE
## logical 1099 11085
summary(rowSums(chimp_lung_exp > 1.5) >= 2)
## Mode FALSE TRUE
## logical 465 11719
summary(rowSums(human_lung_exp > 1.5) >= 2)
## Mode FALSE TRUE
## logical 384 11800
summary(rowSums(rhesus_lung_exp > 1.5) >= 2)
## Mode FALSE TRUE
## logical 604 11580
summary(rowSums(chimp_heart_exp > 0) >= 1)
## Mode FALSE TRUE
## logical 103 12081
summary(rowSums(human_heart_exp > 0) >= 1)
## Mode FALSE TRUE
## logical 88 12096
summary(rowSums(rhesus_heart_exp > 0) >= 1)
## Mode FALSE TRUE
## logical 240 11944
summary(rowSums(chimp_kidney_exp > 0) >= 1)
## Mode FALSE TRUE
## logical 36 12148
summary(rowSums(human_kidney_exp > 0) >= 1)
## Mode FALSE TRUE
## logical 26 12158
summary(rowSums(rhesus_kidney_exp > 0) >= 1)
## Mode FALSE TRUE
## logical 134 12050
summary(rowSums(chimp_liver_exp > 0) >= 1)
## Mode FALSE TRUE
## logical 96 12088
summary(rowSums(human_liver_exp > 0) >= 1)
## Mode FALSE TRUE
## logical 43 12141
summary(rowSums(rhesus_liver_exp > 0) >= 1)
## Mode FALSE TRUE
## logical 273 11911
summary(rowSums(chimp_lung_exp > 0) >= 1)
## Mode FALSE TRUE
## logical 54 12130
summary(rowSums(human_lung_exp > 0) >= 1)
## Mode FALSE TRUE
## logical 26 12158
summary(rowSums(rhesus_lung_exp > 0) >= 1)
## Mode FALSE TRUE
## logical 112 12072