Recapitulate observed/expected/pvalue from Pai et al. 2011

Calculating the observed versus expected from Figure 3 Pai et al. 2011

Liver specific

m <- 470+367
n <- 9911-(470+367)
x <- 367
q = x
k <- (603+367)
phyper(q, m, n, k, lower.tail = FALSE)
## [1] 5.41205e-170
dhyper(1:x, m, n, k)
##   [1]  6.188428e-38  3.092244e-36  1.027671e-34  2.555483e-33  5.071750e-32
##   [6]  8.368283e-31  1.180707e-29  1.454214e-28  1.588305e-27  1.557589e-26
##  [11]  1.385314e-25  1.126740e-24  8.439257e-24  5.855531e-23  3.782947e-22
##  [16]  2.285753e-21  1.296769e-20  6.931604e-20  3.501745e-19  1.676558e-18
##  [21]  7.626433e-18  3.303531e-17  1.365483e-16  5.395922e-16  2.042068e-15
##  [26]  7.413002e-15  2.585111e-14  8.672026e-14  2.802020e-13  8.730654e-13
##  [31]  2.626207e-12  7.634289e-12  2.146788e-11  5.845049e-11  1.542199e-10
##  [36]  3.946385e-10  9.801655e-10  2.364593e-09  5.544597e-09  1.264517e-08
##  [41]  2.806669e-08  6.066333e-08  1.277542e-07  2.622839e-07  5.252173e-07
##  [46]  1.026338e-06  1.958079e-06  3.648830e-06  6.644281e-06  1.182750e-05
##  [51]  2.059025e-05  3.506865e-05  5.845546e-05  9.539662e-05  1.524722e-04
##  [56]  2.387483e-04  3.663695e-04  5.511376e-04  8.130000e-04  1.176344e-03
##  [61]  1.669978e-03  2.326672e-03  3.182143e-03  4.273387e-03  5.636346e-03
##  [66]  7.302936e-03  9.297588e-03  1.163353e-02  1.430915e-02  1.730482e-02
##  [71]  2.058064e-02  2.407543e-02  2.770734e-02  3.137631e-02  3.496817e-02
##  [76]  3.836048e-02  4.142945e-02  4.405753e-02  4.614101e-02  4.759687e-02
##  [81]  4.836827e-02  4.842822e-02  4.778104e-02  4.646152e-02  4.453201e-02
##  [86]  4.207761e-02  3.920009e-02  3.601111e-02  3.262525e-02  2.915365e-02
##  [91]  2.569839e-02  2.234826e-02  1.917594e-02  1.623654e-02  1.356756e-02
##  [96]  1.118997e-02  9.110031e-03  7.321835e-03  5.809958e-03  4.552205e-03
## [101]  3.522156e-03  2.691377e-03  2.031234e-03  1.514274e-03  1.115184e-03
## [106]  8.113811e-04  5.832788e-04  4.143212e-04  2.908330e-04  2.017580e-04
## [111]  1.383353e-04  9.375283e-05  6.280843e-05  4.159742e-05  2.723715e-05
## [116]  1.763336e-05  1.128802e-05  7.145618e-06  4.473331e-06  2.769623e-06
## [121]  1.696045e-06  1.027329e-06  6.155523e-07  3.648636e-07  2.139604e-07
## [126]  1.241366e-07  7.126158e-08  4.047865e-08  2.275289e-08  1.265644e-08
## [131]  6.967475e-09  3.796224e-09  2.047219e-09  1.092788e-09  5.774164e-10
## [136]  3.020275e-10  1.563976e-10  8.017916e-11  4.069695e-11  2.045278e-11
## [141]  1.017779e-11  5.015168e-12  2.447195e-12  1.182558e-12  5.659348e-13
## [146]  2.682376e-13  1.259218e-13  5.855028e-14  2.696633e-14  1.230262e-14
## [151]  5.559994e-15  2.489253e-15  1.104077e-15  4.851565e-16  2.112193e-16
## [156]  9.111101e-17  3.894127e-17  1.649177e-17  6.920830e-18  2.878051e-18
## [161]  1.186051e-18  4.843822e-19  1.960504e-19  7.864243e-20  3.126584e-20
## [166]  1.232031e-20  4.812001e-21  1.862929e-21  7.149028e-22  2.719516e-22
## [171]  1.025518e-22  3.833675e-23  1.420760e-23  5.220025e-24  1.901443e-24
## [176]  6.866973e-25  2.458846e-25  8.729576e-26  3.073003e-26  1.072637e-26
## [181]  3.712566e-27  1.274203e-27  4.336684e-28  1.463669e-28  4.898968e-29
## [186]  1.626127e-29  5.353070e-30  1.747676e-30  5.658989e-31  1.817386e-31
## [191]  5.788904e-32  1.828927e-32  5.731355e-33  1.781513e-33  5.492896e-34
## [196]  1.679979e-34  5.096902e-35  1.533973e-35  4.579814e-36  1.356456e-36
## [201]  3.985658e-37  1.161824e-37  3.359966e-38  9.640351e-39  2.744244e-39
## [206]  7.750558e-40  2.171861e-40  6.038489e-41  1.665827e-41  4.559790e-42
## [211]  1.238458e-42  3.337698e-43  8.925857e-44  2.368633e-44  6.237319e-45
## [216]  1.629890e-45  4.226549e-46  1.087648e-46  2.777620e-47  7.039576e-48
## [221]  1.770584e-48  4.419667e-49  1.094896e-49  2.691988e-50  6.568966e-51
## [226]  1.590931e-51  3.824216e-52  9.123826e-53  2.160535e-53  5.078106e-54
## [231]  1.184690e-54  2.743317e-55  6.305536e-56  1.438629e-56  3.258082e-57
## [236]  7.324327e-58  1.634451e-58  3.620594e-59  7.961550e-60  1.737924e-60
## [241]  3.766036e-61  8.101483e-62  1.730120e-62  3.667961e-63  7.719968e-64
## [246]  1.613072e-64  3.346141e-65  6.891161e-66  1.408974e-66  2.860100e-67
## [251]  5.764101e-68  1.153345e-68  2.291229e-69  4.519230e-70  8.850168e-71
## [256]  1.720815e-71  3.322135e-72  6.368028e-73  1.211997e-73  2.290402e-74
## [261]  4.297733e-75  8.007353e-76  1.481374e-76  2.721262e-77  4.963753e-78
## [266]  8.990591e-79  1.616994e-79  2.887849e-80  5.121422e-81  9.019037e-82
## [271]  1.577202e-82  2.738894e-83  4.723109e-84  8.088144e-85  1.375440e-85
## [276]  2.322788e-86  3.895439e-87  6.487617e-88  1.072999e-88  1.762391e-89
## [281]  2.874731e-90  4.656797e-91  7.491619e-92  1.196921e-92  1.899151e-93
## [286]  2.992687e-94  4.683530e-95  7.279453e-96  1.123674e-96  1.722666e-97
## [291]  2.622912e-98  3.966348e-99 5.956967e-100 8.885658e-101 1.316396e-101
## [296] 1.936951e-102 2.830664e-103 4.108641e-104 5.923122e-105 8.481022e-106
## [301] 1.206127e-106 1.703678e-107 2.390200e-108 3.330696e-109 4.609908e-110
## [306] 6.337356e-111 8.653359e-112 1.173611e-112 1.580987e-113 2.115435e-114
## [311] 2.811510e-115 3.711509e-116 4.866694e-117 6.338582e-118 8.200240e-119
## [316] 1.053754e-119 1.345029e-120 1.705320e-121 2.147649e-122 2.686617e-123
## [321] 3.338372e-124 4.120518e-125 5.051944e-126 6.152567e-127 7.442980e-128
## [326] 8.943991e-129 1.067607e-129 1.265867e-130 1.490949e-131 1.744364e-132
## [331] 2.027271e-133 2.340392e-134 2.683912e-135 3.057401e-136 3.459725e-137
## [336] 3.888995e-138 4.342507e-139 4.816729e-140 5.307296e-141 5.809047e-142
## [341] 6.316083e-143 6.821862e-144 7.319327e-145 7.801055e-146 8.259432e-147
## [346] 8.686853e-148 9.075927e-149 9.419685e-150 9.711791e-151 9.946733e-152
## [351] 1.012000e-152 1.022821e-153 1.026925e-154 1.024232e-155 1.014796e-156
## [356] 9.988049e-158 9.765719e-159 9.485274e-160 9.152043e-161 8.772209e-162
## [361] 8.352626e-163 7.900607e-164 7.423718e-165 6.929569e-166 6.425620e-167
## [366] 5.918994e-168 5.416328e-169
max(dhyper(1:x, m, n, k))
## [1] 0.04842822
plot(dhyper(1:x, m, n, k))

which(grepl(max(dhyper(1:x, m, n, k)), dhyper(1:x, m, n, k)))
## [1] 82

Kidney specific

m <- 85+127
n <- 9911-(85+127)
x <- 85
q = x
k <- (129+85)
phyper(q, m, n, k, lower.tail = FALSE)
## [1] 2.782087e-92
dhyper(1:x, m, n, k)
##  [1] 4.445744e-02 1.053047e-01 1.647050e-01 1.913618e-01 1.761577e-01
##  [6] 1.338305e-01 8.630377e-02 4.822370e-02 2.371735e-02 1.039492e-02
## [11] 4.100806e-03 1.468228e-03 4.803961e-04 1.444916e-04 4.015346e-05
## [16] 1.035507e-05 2.487771e-06 5.586991e-07 1.176456e-07 2.329086e-08
## [21] 4.345816e-09 7.659420e-10 1.277714e-10 2.021077e-11 3.036503e-12
## [26] 4.339879e-13 5.908983e-14 7.674509e-15 9.519633e-16 1.129049e-16
## [31] 1.281699e-17 1.394009e-18 1.453951e-19 1.455497e-20 1.399583e-21
## [36] 1.293719e-22 1.150384e-23 9.846837e-25 8.118479e-26 6.451101e-27
## [41] 4.943301e-28 3.654718e-29 2.608321e-30 1.797810e-31 1.197282e-32
## [46] 7.707322e-34 4.797765e-35 2.889140e-36 1.683640e-37 9.497955e-39
## [51] 5.188628e-40 2.745686e-41 1.407838e-42 6.996472e-44 3.370894e-45
## [56] 1.574925e-46 7.137192e-48 3.137949e-49 1.338778e-50 5.543763e-52
## [61] 2.228526e-53 8.698161e-55 3.296927e-56 1.213765e-57 4.340812e-59
## [66] 1.508279e-60 5.092455e-62 1.670952e-63 5.328990e-65 1.652039e-66
## [71] 4.978936e-68 1.458941e-69 4.156847e-71 1.151738e-72 3.103429e-74
## [76] 8.133177e-76 2.073188e-77 5.140488e-79 1.239885e-80 2.909322e-82
## [81] 6.641332e-84 1.474988e-85 3.187179e-87 6.700723e-89 1.370705e-90
max(dhyper(1:x, m, n, k))
## [1] 0.1913618
plot(dhyper(1:x, m, n, k))

which(grepl(max(dhyper(1:x, m, n, k)), dhyper(1:x, m, n, k)))
## [1] 4

Heart specific

m <- 112+240
n <- 9911-(112+240)
x <- 112
q = x
k <- (282+112)
phyper(q, m, n, k, lower.tail = FALSE)
## [1] 6.770081e-75
dhyper(1:x, m, n, k)
##   [1] 7.306062e-06 5.497000e-05 2.742105e-04 1.020244e-03 3.020013e-03
##   [6] 7.408323e-03 1.549051e-02 2.818346e-02 4.532510e-02 6.523604e-02
##  [11] 8.487872e-02 1.006630e-01 1.095774e-01 1.101342e-01 1.027279e-01
##  [16] 8.931978e-02 7.267625e-02 5.552922e-02 3.996413e-02 2.716669e-02
##  [21] 1.748641e-02 1.068172e-02 6.205106e-03 3.434310e-03 1.814093e-03
##  [26] 9.160044e-04 4.427812e-04 2.051745e-04 9.125295e-05 3.900042e-05
##  [31] 1.603489e-05 6.348651e-06 2.422884e-06 8.920947e-07 3.171646e-07
##  [36] 1.089685e-07 3.620654e-08 1.164268e-08 3.625695e-09 1.094158e-09
##  [41] 3.201719e-10 9.089727e-11 2.505079e-11 6.705357e-12 1.744088e-12
##  [46] 4.410295e-13 1.084717e-13 2.595993e-14 6.047961e-15 1.372162e-15
##  [51] 3.032900e-16 6.533197e-17 1.372020e-17 2.810014e-18 5.614488e-19
##  [56] 1.094713e-19 2.083573e-20 3.872223e-21 7.028711e-22 1.246437e-22
##  [61] 2.160014e-23 3.658824e-24 6.059398e-25 9.813427e-26 1.554576e-26
##  [66] 2.409335e-27 3.653982e-28 5.423845e-29 7.881417e-30 1.121345e-30
##  [71] 1.562396e-31 2.132241e-32 2.850687e-33 3.734238e-34 4.793620e-35
##  [76] 6.031168e-36 7.438425e-37 8.994258e-38 1.066390e-38 1.239916e-39
##  [81] 1.414008e-40 1.581797e-41 1.735974e-42 1.869312e-43 1.975230e-44
##  [86] 2.048332e-45 2.084864e-46 2.083036e-47 2.043161e-48 1.967611e-49
##  [91] 1.860585e-50 1.727725e-51 1.575632e-52 1.411331e-53 1.241753e-54
##  [96] 1.073274e-55 9.113607e-57 7.603423e-58 6.233054e-59 5.021090e-60
## [101] 3.974955e-61 3.092674e-62 2.365014e-63 1.777706e-64 1.313532e-65
## [106] 9.541198e-67 6.813548e-68 4.783847e-69 3.302475e-70 2.241734e-71
## [111] 1.496353e-72 9.822272e-74
max(dhyper(1:x, m, n, k))
## [1] 0.1101342
plot(dhyper(1:x, m, n, k))

which(grepl(max(dhyper(1:x, m, n, k)), dhyper(1:x, m, n, k)))
## [1] 14

Comparison to Joyce’s Method

# Liver specific

which(grepl(max(dhyper(1:367, m=970, n=9911-970, k=837)), dhyper(1:367, m=970, n=9911-970, k=837)))
## [1] 82
phyper(367, m=970, n=9911-970, k=837, lower.tail = FALSE)
## [1] 5.41205e-170
# Kidney specific

which(grepl(max(dhyper(1:85, m=129+85, n=9911-129-85, k=127+85)), dhyper(1:85, m=129+85, n=9911-129-85, k=127+85)))
## [1] 4
phyper(85, m=129+85, n=9911-129-85, k=127+85, lower.tail = FALSE)
## [1] 2.782087e-92
# Heart specific 

which(grepl(max(dhyper(1:112, m=282+112, n=9911-282-112, k=112+240)), dhyper(1:112, m=282+112, n=9911-282-112, k=112+240)))
## [1] 14
phyper(112, m=282+112, n=9911-282-112, k=112+240, lower.tail = FALSE)
## [1] 6.770081e-75