batchqc_explained_variation: Returns a list of explained variation by batch and condition...
In BatchQC: Batch Effects Quality Control Software
Description
Usage
Arguments
Value
Examples
Description
Returns a list of explained variation by batch and condition
combinations
Usage
1
Arguments
data.matrix
Given data or simulated data from rnaseq_sim()
condition
Condition covariate of interest
batch
Batch covariate
Value
List of explained variation by batch and condition
Examples
1
2
3
4
5
6
7
8
9
nbatch <- 3
ncond <- 2
npercond <- 10
data.matrix <- rnaseq_sim(ngenes=50, nbatch=nbatch, ncond=ncond, npercond=
npercond, basemean=10000, ggstep=50, bbstep=2000, ccstep=800,
basedisp=100, bdispstep=-10, swvar=1000, seed=1234)
batch <- rep(1:nbatch, each=ncond*npercond)
condition <- rep(rep(1:ncond, each=npercond), nbatch)
batchqc_explained_variation(data.matrix, condition, batch)
Example output
sh: 1: cannot create /dev/null: Permission denied
$explained_variation
Full (Condition+Batch) Condition Batch
[1,] 64.077 7.624 56.453
[2,] 59.607 2.042 57.565
[3,] 55.849 3.161 52.688
[4,] 61.101 5.683 55.418
[5,] 62.141 15.230 46.911
[6,] 60.554 1.998 58.556
[7,] 60.531 4.564 55.967
[8,] 59.776 11.091 48.685
[9,] 63.923 7.921 56.002
[10,] 59.949 2.093 57.856
[11,] 53.062 3.154 49.908
[12,] 54.984 4.677 50.307
[13,] 70.431 2.218 68.213
[14,] 56.503 0.244 56.259
[15,] 62.770 0.059 62.711
[16,] 62.288 2.773 59.515
[17,] 59.647 3.051 56.597
[18,] 47.522 0.116 47.405
[19,] 54.346 0.596 53.749
[20,] 57.865 0.834 57.031
[21,] 68.832 5.546 63.286
[22,] 58.925 9.020 49.906
[23,] 58.042 10.956 47.086
[24,] 65.218 0.638 64.580
[25,] 56.683 1.327 55.355
[26,] 57.182 0.222 56.961
[27,] 66.413 1.844 64.570
[28,] 66.266 2.542 63.723
[29,] 63.170 0.766 62.405
[30,] 60.842 11.693 49.149
[31,] 51.967 2.013 49.953
[32,] 59.869 5.473 54.396
[33,] 59.701 5.566 54.134
[34,] 61.656 0.048 61.608
[35,] 58.229 2.808 55.421
[36,] 54.031 7.651 46.379
[37,] 64.116 10.187 53.929
[38,] 49.174 2.830 46.344
[39,] 53.007 1.546 51.461
[40,] 43.998 1.105 42.893
[41,] 43.736 0.704 43.032
[42,] 52.987 10.866 42.121
[43,] 59.272 6.241 53.031
[44,] 56.256 0.000 56.256
[45,] 53.095 12.686 40.409
[46,] 58.429 7.857 50.572
[47,] 63.650 9.986 53.663
[48,] 49.674 2.685 46.989
[49,] 53.785 1.198 52.587
[50,] 54.584 1.465 53.119
$cond_test
$cond_test$p
[1] 1.080761e-03 9.805442e-02 5.009892e-02 5.938615e-03 1.474482e-05
[6] 9.771106e-02 1.372024e-02 2.362724e-04 9.020723e-04 9.269789e-02
[11] 5.742862e-02 1.916120e-02 4.512224e-02 5.770584e-01 7.663521e-01
[16] 4.719286e-02 4.429591e-02 7.260847e-01 3.960370e-01 2.970655e-01
[21] 2.569096e-03 9.014702e-04 3.323115e-04 3.152548e-01 1.955554e-01
[26] 5.923679e-01 8.503170e-02 4.462188e-02 2.852558e-01 1.398053e-04
[31] 1.311201e-01 7.724582e-03 7.365440e-03 7.927532e-01 5.738764e-02
[36] 3.462544e-03 1.956944e-04 8.287499e-02 1.801648e-01 2.976561e-01
[41] 4.060412e-01 6.803778e-04 4.906950e-03 9.998841e-01 2.670574e-04
[46] 1.936276e-03 2.417993e-04 8.940921e-02 2.332875e-01 1.843663e-01
$cond_test$r2_full
[1] 0.6407732 0.5960681 0.5584881 0.6110051 0.6214115 0.6055439 0.6053102
[8] 0.5977573 0.6392346 0.5994908 0.5306213 0.5498396 0.7043092 0.5650338
[15] 0.6276978 0.6228842 0.5964737 0.4752157 0.5434573 0.5786469 0.6883171
[22] 0.5892521 0.5804237 0.6521787 0.5668256 0.5718243 0.6641324 0.6626557
[29] 0.6317042 0.6084193 0.5196653 0.5986872 0.5970058 0.6165561 0.5822937
[36] 0.5403065 0.6411591 0.4917442 0.5300656 0.4399835 0.4373578 0.5298705
[43] 0.5927199 0.5625620 0.5309488 0.5842863 0.6364989 0.4967355 0.5378507
[50] 0.5458417
$cond_test$r2_reduced
[1] 0.5645327 0.5756511 0.5268775 0.5541769 0.4691107 0.5855640 0.5596701
[8] 0.4868486 0.5600234 0.5785641 0.4990774 0.5030682 0.6821331 0.5625896
[15] 0.6271051 0.5951529 0.5659664 0.4740539 0.5374936 0.5703111 0.6328553
[22] 0.4990553 0.4708630 0.6458007 0.5535518 0.5696071 0.6456963 0.6372327
[29] 0.6240487 0.4914940 0.4995304 0.5439585 0.5413430 0.6160789 0.5542129
[36] 0.4637928 0.5392905 0.4634437 0.5146083 0.4289318 0.4303158 0.4212139
[43] 0.5303141 0.5625620 0.4040902 0.5057200 0.5366346 0.4698854 0.5258685
[50] 0.5311923
$batch_test
$batch_test$p
[1] 3.270939e-12 1.688383e-11 2.811813e-10 1.697797e-11 1.577315e-10
[6] 8.578027e-12 1.833267e-11 2.265534e-10 4.034773e-12 1.349965e-11
[11] 1.557457e-09 7.529499e-10 2.886580e-15 8.063283e-11 9.823253e-13
[16] 3.042788e-12 2.193645e-11 1.491418e-08 3.453153e-10 3.907363e-11
[21] 3.297362e-14 2.135903e-10 7.075962e-10 1.720846e-13 9.751033e-11
[26] 5.157141e-11 9.103829e-14 1.256772e-13 8.850698e-13 1.291425e-10
[31] 2.140791e-09 3.818934e-11 4.413747e-11 2.235989e-12 5.379541e-11
[36] 3.288980e-09 6.978085e-12 1.316468e-08 1.015020e-09 1.215523e-07
[41] 1.237201e-07 1.662757e-08 7.254219e-11 8.823919e-11 2.778429e-08
[46] 2.095299e-10 9.408918e-12 9.577759e-09 5.760901e-10 3.812951e-10
$batch_test$r2_full
[1] 0.6407732 0.5960681 0.5584881 0.6110051 0.6214115 0.6055439 0.6053102
[8] 0.5977573 0.6392346 0.5994908 0.5306213 0.5498396 0.7043092 0.5650338
[15] 0.6276978 0.6228842 0.5964737 0.4752157 0.5434573 0.5786469 0.6883171
[22] 0.5892521 0.5804237 0.6521787 0.5668256 0.5718243 0.6641324 0.6626557
[29] 0.6317042 0.6084193 0.5196653 0.5986872 0.5970058 0.6165561 0.5822937
[36] 0.5403065 0.6411591 0.4917442 0.5300656 0.4399835 0.4373578 0.5298705
[43] 0.5927199 0.5625620 0.5309488 0.5842863 0.6364989 0.4967355 0.5378507
[50] 0.5458417
$batch_test$r2_reduced
[1] 7.624052e-02 2.041704e-02 3.161060e-02 5.682817e-02 1.523008e-01
[6] 1.997993e-02 4.564015e-02 1.109086e-01 7.921127e-02 2.092667e-02
[11] 3.154384e-02 4.677143e-02 2.217616e-02 2.444224e-03 5.927627e-04
[16] 2.773135e-02 3.050734e-02 1.161785e-03 5.963715e-03 8.335812e-03
[21] 5.546189e-02 9.019683e-02 1.095607e-01 6.377949e-03 1.327380e-02
[26] 2.217181e-03 1.843602e-02 2.542299e-02 7.655513e-03 1.169253e-01
[31] 2.013485e-02 5.472874e-02 5.566287e-02 4.772039e-04 2.808082e-02
[36] 7.651365e-02 1.018686e-01 2.830046e-02 1.545727e-02 1.105173e-02
[41] 7.042037e-03 1.086566e-01 6.240581e-02 1.662415e-10 1.268586e-01
[46] 7.856630e-02 9.986433e-02 2.685016e-02 1.198222e-02 1.464947e-02
BatchQC documentation built on Nov. 8, 2020, 8:30 p.m.
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Description Usage Arguments Value Examples
Description
Returns a list of explained variation by batch and condition combinations
Usage
1 |
Arguments
data.matrix |
Given data or simulated data from rnaseq_sim() |
condition |
Condition covariate of interest |
batch |
Batch covariate |
Value
List of explained variation by batch and condition
Examples
1 2 3 4 5 6 7 8 9 | nbatch <- 3
ncond <- 2
npercond <- 10
data.matrix <- rnaseq_sim(ngenes=50, nbatch=nbatch, ncond=ncond, npercond=
npercond, basemean=10000, ggstep=50, bbstep=2000, ccstep=800,
basedisp=100, bdispstep=-10, swvar=1000, seed=1234)
batch <- rep(1:nbatch, each=ncond*npercond)
condition <- rep(rep(1:ncond, each=npercond), nbatch)
batchqc_explained_variation(data.matrix, condition, batch)
|
Example output
sh: 1: cannot create /dev/null: Permission denied
$explained_variation
Full (Condition+Batch) Condition Batch
[1,] 64.077 7.624 56.453
[2,] 59.607 2.042 57.565
[3,] 55.849 3.161 52.688
[4,] 61.101 5.683 55.418
[5,] 62.141 15.230 46.911
[6,] 60.554 1.998 58.556
[7,] 60.531 4.564 55.967
[8,] 59.776 11.091 48.685
[9,] 63.923 7.921 56.002
[10,] 59.949 2.093 57.856
[11,] 53.062 3.154 49.908
[12,] 54.984 4.677 50.307
[13,] 70.431 2.218 68.213
[14,] 56.503 0.244 56.259
[15,] 62.770 0.059 62.711
[16,] 62.288 2.773 59.515
[17,] 59.647 3.051 56.597
[18,] 47.522 0.116 47.405
[19,] 54.346 0.596 53.749
[20,] 57.865 0.834 57.031
[21,] 68.832 5.546 63.286
[22,] 58.925 9.020 49.906
[23,] 58.042 10.956 47.086
[24,] 65.218 0.638 64.580
[25,] 56.683 1.327 55.355
[26,] 57.182 0.222 56.961
[27,] 66.413 1.844 64.570
[28,] 66.266 2.542 63.723
[29,] 63.170 0.766 62.405
[30,] 60.842 11.693 49.149
[31,] 51.967 2.013 49.953
[32,] 59.869 5.473 54.396
[33,] 59.701 5.566 54.134
[34,] 61.656 0.048 61.608
[35,] 58.229 2.808 55.421
[36,] 54.031 7.651 46.379
[37,] 64.116 10.187 53.929
[38,] 49.174 2.830 46.344
[39,] 53.007 1.546 51.461
[40,] 43.998 1.105 42.893
[41,] 43.736 0.704 43.032
[42,] 52.987 10.866 42.121
[43,] 59.272 6.241 53.031
[44,] 56.256 0.000 56.256
[45,] 53.095 12.686 40.409
[46,] 58.429 7.857 50.572
[47,] 63.650 9.986 53.663
[48,] 49.674 2.685 46.989
[49,] 53.785 1.198 52.587
[50,] 54.584 1.465 53.119
$cond_test
$cond_test$p
[1] 1.080761e-03 9.805442e-02 5.009892e-02 5.938615e-03 1.474482e-05
[6] 9.771106e-02 1.372024e-02 2.362724e-04 9.020723e-04 9.269789e-02
[11] 5.742862e-02 1.916120e-02 4.512224e-02 5.770584e-01 7.663521e-01
[16] 4.719286e-02 4.429591e-02 7.260847e-01 3.960370e-01 2.970655e-01
[21] 2.569096e-03 9.014702e-04 3.323115e-04 3.152548e-01 1.955554e-01
[26] 5.923679e-01 8.503170e-02 4.462188e-02 2.852558e-01 1.398053e-04
[31] 1.311201e-01 7.724582e-03 7.365440e-03 7.927532e-01 5.738764e-02
[36] 3.462544e-03 1.956944e-04 8.287499e-02 1.801648e-01 2.976561e-01
[41] 4.060412e-01 6.803778e-04 4.906950e-03 9.998841e-01 2.670574e-04
[46] 1.936276e-03 2.417993e-04 8.940921e-02 2.332875e-01 1.843663e-01
$cond_test$r2_full
[1] 0.6407732 0.5960681 0.5584881 0.6110051 0.6214115 0.6055439 0.6053102
[8] 0.5977573 0.6392346 0.5994908 0.5306213 0.5498396 0.7043092 0.5650338
[15] 0.6276978 0.6228842 0.5964737 0.4752157 0.5434573 0.5786469 0.6883171
[22] 0.5892521 0.5804237 0.6521787 0.5668256 0.5718243 0.6641324 0.6626557
[29] 0.6317042 0.6084193 0.5196653 0.5986872 0.5970058 0.6165561 0.5822937
[36] 0.5403065 0.6411591 0.4917442 0.5300656 0.4399835 0.4373578 0.5298705
[43] 0.5927199 0.5625620 0.5309488 0.5842863 0.6364989 0.4967355 0.5378507
[50] 0.5458417
$cond_test$r2_reduced
[1] 0.5645327 0.5756511 0.5268775 0.5541769 0.4691107 0.5855640 0.5596701
[8] 0.4868486 0.5600234 0.5785641 0.4990774 0.5030682 0.6821331 0.5625896
[15] 0.6271051 0.5951529 0.5659664 0.4740539 0.5374936 0.5703111 0.6328553
[22] 0.4990553 0.4708630 0.6458007 0.5535518 0.5696071 0.6456963 0.6372327
[29] 0.6240487 0.4914940 0.4995304 0.5439585 0.5413430 0.6160789 0.5542129
[36] 0.4637928 0.5392905 0.4634437 0.5146083 0.4289318 0.4303158 0.4212139
[43] 0.5303141 0.5625620 0.4040902 0.5057200 0.5366346 0.4698854 0.5258685
[50] 0.5311923
$batch_test
$batch_test$p
[1] 3.270939e-12 1.688383e-11 2.811813e-10 1.697797e-11 1.577315e-10
[6] 8.578027e-12 1.833267e-11 2.265534e-10 4.034773e-12 1.349965e-11
[11] 1.557457e-09 7.529499e-10 2.886580e-15 8.063283e-11 9.823253e-13
[16] 3.042788e-12 2.193645e-11 1.491418e-08 3.453153e-10 3.907363e-11
[21] 3.297362e-14 2.135903e-10 7.075962e-10 1.720846e-13 9.751033e-11
[26] 5.157141e-11 9.103829e-14 1.256772e-13 8.850698e-13 1.291425e-10
[31] 2.140791e-09 3.818934e-11 4.413747e-11 2.235989e-12 5.379541e-11
[36] 3.288980e-09 6.978085e-12 1.316468e-08 1.015020e-09 1.215523e-07
[41] 1.237201e-07 1.662757e-08 7.254219e-11 8.823919e-11 2.778429e-08
[46] 2.095299e-10 9.408918e-12 9.577759e-09 5.760901e-10 3.812951e-10
$batch_test$r2_full
[1] 0.6407732 0.5960681 0.5584881 0.6110051 0.6214115 0.6055439 0.6053102
[8] 0.5977573 0.6392346 0.5994908 0.5306213 0.5498396 0.7043092 0.5650338
[15] 0.6276978 0.6228842 0.5964737 0.4752157 0.5434573 0.5786469 0.6883171
[22] 0.5892521 0.5804237 0.6521787 0.5668256 0.5718243 0.6641324 0.6626557
[29] 0.6317042 0.6084193 0.5196653 0.5986872 0.5970058 0.6165561 0.5822937
[36] 0.5403065 0.6411591 0.4917442 0.5300656 0.4399835 0.4373578 0.5298705
[43] 0.5927199 0.5625620 0.5309488 0.5842863 0.6364989 0.4967355 0.5378507
[50] 0.5458417
$batch_test$r2_reduced
[1] 7.624052e-02 2.041704e-02 3.161060e-02 5.682817e-02 1.523008e-01
[6] 1.997993e-02 4.564015e-02 1.109086e-01 7.921127e-02 2.092667e-02
[11] 3.154384e-02 4.677143e-02 2.217616e-02 2.444224e-03 5.927627e-04
[16] 2.773135e-02 3.050734e-02 1.161785e-03 5.963715e-03 8.335812e-03
[21] 5.546189e-02 9.019683e-02 1.095607e-01 6.377949e-03 1.327380e-02
[26] 2.217181e-03 1.843602e-02 2.542299e-02 7.655513e-03 1.169253e-01
[31] 2.013485e-02 5.472874e-02 5.566287e-02 4.772039e-04 2.808082e-02
[36] 7.651365e-02 1.018686e-01 2.830046e-02 1.545727e-02 1.105173e-02
[41] 7.042037e-03 1.086566e-01 6.240581e-02 1.662415e-10 1.268586e-01
[46] 7.856630e-02 9.986433e-02 2.685016e-02 1.198222e-02 1.464947e-02
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