library(tidyverse)
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options(stringsAsFactors = FALSE);
# http://ftp.ebi.ac.uk/ensemblgenomes/pub/release-52/plants/gtf/lupinus_angustifolius/Lupinus_angustifolius.LupAngTanjil_v1.0.52.gtf.gz
download.file("http://ziemann-lab.net/public/barry/3col.tsv.gz",destfile = "3col.tsv.gz")
c3 <- read.table("3col.tsv.gz")
head(c3)
## V1 V2 V3
## 1 BS01_S2_R1_001.ReadsPerGene.out.tab IUM83_01698 0
## 2 BS01_S2_R1_001.ReadsPerGene.out.tab IUM83_01699 0
## 3 BS01_S2_R1_001.ReadsPerGene.out.tab IUM83_01700 0
## 4 BS01_S2_R1_001.ReadsPerGene.out.tab IUM83_01701 0
## 5 BS01_S2_R1_001.ReadsPerGene.out.tab IUM83_01702 0
## 6 BS01_S2_R1_001.ReadsPerGene.out.tab IUM83_01703 0
x <- t(acast(c3, V1~V2, value.var="V3"))
head(x)
## BS01_S2_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 3
## ENSRNA049758853 0
## BS02_S3_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 1
## ENSRNA049758853 0
## BS03_S4_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 1
## ENSRNA049758853 0
## BS04_S5_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 1
## ENSRNA049758851 1
## ENSRNA049758853 0
## BS05_S6_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 2
## ENSRNA049758853 0
## BS06_S7_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 1
## ENSRNA049758853 0
## BS07_S8_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 0
## ENSRNA049758853 0
## BS08_S9_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 0
## ENSRNA049758853 0
## BS09_S10_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 2
## ENSRNA049758853 0
## BS10_S11_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 2
## ENSRNA049758853 0
## BS11_S12_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 2
## ENSRNA049758853 0
## BS12_S13_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 1
## ENSRNA049758848 0
## ENSRNA049758851 3
## ENSRNA049758853 0
## BS13_S14_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 0
## ENSRNA049758853 0
## BS14_S15_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 0
## ENSRNA049758853 0
## BS15_S16_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 0
## ENSRNA049758853 0
## BS16_S17_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 0
## ENSRNA049758853 0
## BS17_S18_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 1
## ENSRNA049758848 0
## ENSRNA049758851 0
## ENSRNA049758853 0
## BS18_S19_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 2
## ENSRNA049758853 0
## BS19_S20_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 0
## ENSRNA049758853 0
## BS20_S21_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 0
## ENSRNA049758853 0
## BS21_S22_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 1
## ENSRNA049758853 0
## BS22_S23_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 0
## ENSRNA049758853 0
## BS23_S24_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 1
## ENSRNA049758853 0
## BS24_S25_R1_001.ReadsPerGene.out.tab
## ENSRNA049758817 0
## ENSRNA049758844 0
## ENSRNA049758846 0
## ENSRNA049758848 0
## ENSRNA049758851 0
## ENSRNA049758853 0
# sample sheet
sample_metadata = read.csv(file = "sample_info.csv")
head(sample_metadata)
## Column1 Column2
## 1 BS01 LaH0_1
## 2 BS02 LaH0_2
## 3 BS03 LaH0_3
## 4 BS04 LaH18_1
## 5 BS05 LaH18_2
## 6 BS06 LaH18_3
colnames(x) <- sample_metadata[,2]
head(x)
## LaH0_1 LaH0_2 LaH0_3 LaH18_1 LaH18_2 LaH18_3 LaH30_1 LaH30_2
## ENSRNA049758817 0 0 0 0 0 0 0 0
## ENSRNA049758844 0 0 0 0 0 0 0 0
## ENSRNA049758846 0 0 0 0 0 0 0 0
## ENSRNA049758848 0 0 0 1 0 0 0 0
## ENSRNA049758851 3 1 1 1 2 1 0 0
## ENSRNA049758853 0 0 0 0 0 0 0 0
## LaH30_3 LaH48_1 LaH48_2 LaH48_3 PcHyp_1 PcHyp_2 PcHyp_3
## ENSRNA049758817 0 0 0 0 0 0 0
## ENSRNA049758844 0 0 0 0 0 0 0
## ENSRNA049758846 0 0 0 1 0 0 0
## ENSRNA049758848 0 0 0 0 0 0 0
## ENSRNA049758851 2 2 2 3 0 0 0
## ENSRNA049758853 0 0 0 0 0 0 0
## LaPc18_1 LaPc18_2 LaPc18_3 LaPc30_1 LaPc30_2 LaPc30_3 LaPc48_1
## ENSRNA049758817 0 0 0 0 0 0 0
## ENSRNA049758844 0 0 0 0 0 0 0
## ENSRNA049758846 0 1 0 0 0 0 0
## ENSRNA049758848 0 0 0 0 0 0 0
## ENSRNA049758851 0 0 2 0 0 1 0
## ENSRNA049758853 0 0 0 0 0 0 0
## LaPc48_2 LaPc48_3
## ENSRNA049758817 0 0
## ENSRNA049758844 0 0
## ENSRNA049758846 0 0
## ENSRNA049758848 0 0
## ENSRNA049758851 1 0
## ENSRNA049758853 0 0
# get rid of controls
x <- x[,16:ncol(x)]
head(x)
## LaPc18_1 LaPc18_2 LaPc18_3 LaPc30_1 LaPc30_2 LaPc30_3 LaPc48_1
## ENSRNA049758817 0 0 0 0 0 0 0
## ENSRNA049758844 0 0 0 0 0 0 0
## ENSRNA049758846 0 1 0 0 0 0 0
## ENSRNA049758848 0 0 0 0 0 0 0
## ENSRNA049758851 0 0 2 0 0 1 0
## ENSRNA049758853 0 0 0 0 0 0 0
## LaPc48_2 LaPc48_3
## ENSRNA049758817 0 0
## ENSRNA049758844 0 0
## ENSRNA049758846 0 0
## ENSRNA049758848 0 0
## ENSRNA049758851 1 0
## ENSRNA049758853 0 0
dim(x)
## [1] 55151 9
x <- x[which(rowMeans(x)>=10),]
dim(x)
## [1] 36444 9
rpm <- x / colSums(x) * 1000000
dim(rpm)
## [1] 36444 9
samplesize <- round(nrow(rpm)/5)
# downsample matrix genes randomly - only for testing
rpm <- rpm[sample(x=1:nrow(rpm),size = samplesize,replace = FALSE),]
dim(rpm)
## [1] 7289 9
heatmap.2(cor(rpm),trace="none")
genecor <- cor(t(rpm))
heatmap.2(cor(t(rpm)),trace="none")
IUM83RxLR <- readLines('IUMRxLR.csv')
IUM83RxLR <- IUM83RxLR[2:length(IUM83RxLR)]
str(IUM83RxLR)
## chr [1:181] "IUM83_15687" "IUM83_00993" "IUM83_19343" "IUM83_13503" ...
length(IUM83RxLR)
## [1] 181
IUM83RxLR <- IUM83RxLR[which(IUM83RxLR %in% rownames(rpm))]
length(IUM83RxLR)
## [1] 16
corselect <- function(i) {
gene <- IUM83RxLR[i]
hist(genecor[,which(colnames(genecor)==gene)])
mycors <- genecor[,which(colnames(genecor)==gene)]
mytopcor <- mycors[which(mycors>0.8)]
mytopcor <- mytopcor[order(-mytopcor)]
return(mytopcor)
}
# test
corselect(2)
## IUM83_01936 IUM83_05384 IUM83_09517 IUM83_00797 IUM83_01785
## 1.0000000 0.9976466 0.9976172 0.9952603 0.9950969
## IUM83_00664 IUM83_00778 IUM83_18170 IUM83_19954 IUM83_15778
## 0.9945967 0.9943795 0.9942897 0.9924673 0.9921780
## IUM83_18971 IUM83_01358 IUM83_17832 IUM83_09947 TanjilG_04791
## 0.9897297 0.9891162 0.9887485 0.9884491 0.9884255
## IUM83_18264 IUM83_05702 IUM83_02233 IUM83_11719 IUM83_11130
## 0.9881649 0.9880508 0.9870495 0.9868225 0.9865124
## IUM83_06082 IUM83_05965 IUM83_01077 IUM83_01171 IUM83_09655
## 0.9859623 0.9853950 0.9853671 0.9852166 0.9848365
## IUM83_14345 IUM83_10839 IUM83_00857 IUM83_10451 IUM83_19951
## 0.9834448 0.9822391 0.9810675 0.9804052 0.9798911
## IUM83_08181 IUM83_00131 IUM83_03695 IUM83_10536 IUM83_07648
## 0.9797931 0.9792148 0.9788460 0.9785923 0.9785786
## IUM83_10014 IUM83_01898 IUM83_05469 TanjilG_31651 IUM83_18266
## 0.9784451 0.9783075 0.9777038 0.9767750 0.9766480
## IUM83_12540 IUM83_12406 TanjilG_12707 IUM83_05157 IUM83_00858
## 0.9759942 0.9759048 0.9759023 0.9752257 0.9751598
## IUM83_10621 IUM83_09610 IUM83_02557 IUM83_07057 IUM83_11723
## 0.9748812 0.9748756 0.9747741 0.9746945 0.9739416
## IUM83_01067 IUM83_12124 IUM83_09316 IUM83_17103 IUM83_15589
## 0.9725646 0.9724476 0.9722284 0.9721769 0.9713480
## IUM83_13840 TanjilG_29644 IUM83_16987 IUM83_07383 IUM83_14711
## 0.9710319 0.9710260 0.9699059 0.9696840 0.9695680
## IUM83_10616 TanjilG_12534 IUM83_05872 IUM83_11443 IUM83_12656
## 0.9690691 0.9688712 0.9688673 0.9688527 0.9687852
## IUM83_16592 IUM83_18934 IUM83_06893 IUM83_11374 IUM83_00285
## 0.9682891 0.9682312 0.9680584 0.9676884 0.9672962
## IUM83_08430 IUM83_05717 IUM83_09824 IUM83_04119 IUM83_18566
## 0.9672682 0.9672209 0.9666458 0.9666209 0.9658921
## IUM83_18933 IUM83_17689 IUM83_12018 IUM83_16952 IUM83_07237
## 0.9657471 0.9650684 0.9650160 0.9647377 0.9646469
## IUM83_07916 IUM83_12654 IUM83_19207 IUM83_01229 IUM83_07864
## 0.9638583 0.9636356 0.9636056 0.9634573 0.9632610
## IUM83_02473 IUM83_10743 IUM83_00498 IUM83_07789 IUM83_10809
## 0.9631243 0.9630033 0.9628025 0.9626926 0.9623944
## IUM83_00502 IUM83_15426 IUM83_11488 IUM83_15865 IUM83_07080
## 0.9620973 0.9615559 0.9613717 0.9611254 0.9608096
## IUM83_05902 IUM83_09609 IUM83_03118 IUM83_16674 IUM83_09015
## 0.9599531 0.9594726 0.9590363 0.9590260 0.9587824
## IUM83_11275 IUM83_05552 IUM83_18938 IUM83_06415 IUM83_00761
## 0.9585882 0.9581417 0.9579860 0.9577128 0.9576712
## IUM83_00799 IUM83_07860 IUM83_00567 IUM83_08416 IUM83_05865
## 0.9576346 0.9575949 0.9574599 0.9574543 0.9571806
## IUM83_19777 IUM83_00501 IUM83_09168 IUM83_05878 IUM83_04037
## 0.9567809 0.9566894 0.9563874 0.9562886 0.9562138
## IUM83_09665 IUM83_17111 IUM83_06083 IUM83_01652 IUM83_14987
## 0.9559438 0.9559301 0.9559242 0.9552321 0.9546786
## IUM83_16979 IUM83_17288 IUM83_15707 TanjilG_15052 IUM83_18497
## 0.9546625 0.9545386 0.9541823 0.9540969 0.9539233
## IUM83_00656 IUM83_05533 IUM83_11534 IUM83_06489 IUM83_10851
## 0.9538808 0.9532206 0.9530665 0.9529336 0.9528627
## IUM83_12504 IUM83_16678 IUM83_04198 IUM83_10435 IUM83_19247
## 0.9527595 0.9526743 0.9521218 0.9518657 0.9518396
## IUM83_08148 IUM83_01780 IUM83_09695 IUM83_01903 IUM83_02651
## 0.9517457 0.9510074 0.9509269 0.9504456 0.9503411
## TanjilG_21810 IUM83_12920 IUM83_09030 IUM83_18446 IUM83_15823
## 0.9502703 0.9500617 0.9500268 0.9498023 0.9496264
## IUM83_04716 IUM83_15857 IUM83_12942 IUM83_18904 IUM83_04905
## 0.9495705 0.9494422 0.9492381 0.9489269 0.9484404
## IUM83_06127 TanjilG_02833 IUM83_00753 IUM83_01260 IUM83_06981
## 0.9481414 0.9478466 0.9477405 0.9476636 0.9475179
## IUM83_11318 IUM83_00543 IUM83_09915 IUM83_03019 IUM83_12415
## 0.9474933 0.9474173 0.9472971 0.9467116 0.9467095
## IUM83_18488 IUM83_18689 IUM83_16349 IUM83_14652 IUM83_01591
## 0.9463840 0.9457812 0.9455130 0.9454504 0.9450723
## IUM83_06822 IUM83_09281 IUM83_05324 IUM83_04372 IUM83_01996
## 0.9448888 0.9448039 0.9446963 0.9446367 0.9445949
## IUM83_17177 IUM83_16718 IUM83_11716 IUM83_03061 IUM83_13380
## 0.9444587 0.9439470 0.9434331 0.9428352 0.9426335
## IUM83_10334 IUM83_08368 IUM83_10281 IUM83_10768 IUM83_06906
## 0.9426125 0.9425900 0.9425834 0.9425735 0.9422737
## IUM83_09534 IUM83_15291 IUM83_00448 IUM83_12789 IUM83_16079
## 0.9422488 0.9421717 0.9421429 0.9420777 0.9420472
## IUM83_08463 IUM83_06603 IUM83_14867 IUM83_12687 IUM83_08365
## 0.9419890 0.9414308 0.9413985 0.9412394 0.9410844
## IUM83_09089 IUM83_16743 IUM83_09322 IUM83_13313 TanjilG_13267
## 0.9408887 0.9408064 0.9406044 0.9405753 0.9403650
## IUM83_07145 IUM83_16508 IUM83_00987 IUM83_01883 IUM83_13842
## 0.9403401 0.9400668 0.9400574 0.9400299 0.9396612
## IUM83_08147 IUM83_15394 IUM83_01576 IUM83_10326 IUM83_02969
## 0.9396164 0.9394635 0.9393833 0.9392840 0.9392135
## IUM83_00615 IUM83_14742 IUM83_13626 IUM83_16448 IUM83_02996
## 0.9391587 0.9390986 0.9390213 0.9390057 0.9389158
## IUM83_05136 IUM83_01540 TanjilG_27176 IUM83_11423 IUM83_05352
## 0.9386788 0.9386751 0.9385670 0.9384921 0.9384016
## IUM83_01543 IUM83_01276 IUM83_04221 IUM83_16781 IUM83_18221
## 0.9383533 0.9380974 0.9380096 0.9380012 0.9376949
## IUM83_07405 IUM83_16190 IUM83_16232 IUM83_00241 IUM83_03147
## 0.9373711 0.9373483 0.9367788 0.9363356 0.9362682
## IUM83_02191 IUM83_18181 IUM83_01521 IUM83_15242 IUM83_07939
## 0.9362080 0.9360605 0.9358701 0.9354921 0.9353489
## IUM83_03370 IUM83_07740 IUM83_15209 IUM83_04945 IUM83_14361
## 0.9352330 0.9351842 0.9350338 0.9348271 0.9348049
## IUM83_07440 IUM83_12983 IUM83_01498 IUM83_06231 IUM83_19724
## 0.9347216 0.9346879 0.9343200 0.9342108 0.9341162
## IUM83_12146 IUM83_13968 IUM83_00627 IUM83_01293 IUM83_09798
## 0.9337473 0.9336755 0.9334075 0.9334042 0.9332895
## IUM83_03275 IUM83_18415 IUM83_18080 IUM83_09269 IUM83_07831
## 0.9331974 0.9330406 0.9329775 0.9329499 0.9329100
## IUM83_00457 IUM83_15513 IUM83_02097 IUM83_09343 IUM83_07180
## 0.9328516 0.9328400 0.9327746 0.9327193 0.9323114
## IUM83_03269 IUM83_10882 TanjilG_24069 IUM83_04427 IUM83_12019
## 0.9321809 0.9321754 0.9321696 0.9320969 0.9317595
## IUM83_12934 IUM83_08358 IUM83_12326 IUM83_05681 IUM83_06963
## 0.9315687 0.9315384 0.9315010 0.9314609 0.9314187
## IUM83_05656 IUM83_04881 IUM83_16169 TanjilG_32927 TanjilG_10660
## 0.9314138 0.9313919 0.9311790 0.9309539 0.9308445
## IUM83_03335 IUM83_13010 IUM83_01389 IUM83_11397 IUM83_11283
## 0.9308325 0.9307585 0.9306514 0.9306323 0.9304116
## IUM83_07777 IUM83_04415 IUM83_00607 IUM83_18746 IUM83_16063
## 0.9303906 0.9301642 0.9298872 0.9298123 0.9295806
## IUM83_05102 IUM83_04839 IUM83_05110 IUM83_16607 IUM83_01613
## 0.9295532 0.9295291 0.9294387 0.9293116 0.9292871
## TanjilG_08580 IUM83_07893 IUM83_14207 IUM83_06035 IUM83_10669
## 0.9292639 0.9292002 0.9290119 0.9286263 0.9284571
## IUM83_14393 IUM83_03610 IUM83_16353 IUM83_05210 IUM83_14966
## 0.9284139 0.9283913 0.9282554 0.9280551 0.9278806
## IUM83_06193 IUM83_04161 IUM83_19837 TanjilG_19130 IUM83_01362
## 0.9278077 0.9277328 0.9276650 0.9274091 0.9273744
## IUM83_00223 IUM83_11588 TanjilG_08705 IUM83_04763 IUM83_05132
## 0.9273420 0.9272991 0.9272519 0.9270922 0.9270438
## TanjilG_07813 IUM83_12457 IUM83_07435 IUM83_10475 IUM83_17235
## 0.9270044 0.9269637 0.9266845 0.9265803 0.9264631
## IUM83_04476 IUM83_10333 IUM83_11436 IUM83_16309 TanjilG_10486
## 0.9263172 0.9262030 0.9260584 0.9258517 0.9258505
## IUM83_01461 IUM83_16814 TanjilG_15140 IUM83_13733 IUM83_18404
## 0.9256979 0.9255059 0.9252453 0.9251474 0.9250828
## IUM83_00871 IUM83_05453 IUM83_17848 IUM83_08249 TanjilG_04889
## 0.9247693 0.9246335 0.9245113 0.9243140 0.9241214
## IUM83_10443 IUM83_14788 IUM83_13922 IUM83_04908 IUM83_05802
## 0.9236373 0.9235216 0.9234110 0.9233748 0.9232597
## IUM83_04702 IUM83_04187 IUM83_01233 IUM83_14268 IUM83_08716
## 0.9230607 0.9225811 0.9225140 0.9223317 0.9222711
## IUM83_08465 IUM83_15646 TanjilG_24929 IUM83_10562 IUM83_03227
## 0.9221311 0.9219938 0.9215079 0.9213518 0.9213119
## IUM83_05716 IUM83_05174 IUM83_13316 IUM83_00880 IUM83_07999
## 0.9212211 0.9210041 0.9207152 0.9207117 0.9206018
## IUM83_15038 IUM83_12162 IUM83_05649 IUM83_06823 IUM83_08121
## 0.9205467 0.9201982 0.9200934 0.9199325 0.9198531
## IUM83_08814 IUM83_14395 IUM83_07715 IUM83_14938 IUM83_15482
## 0.9198293 0.9198052 0.9197348 0.9194250 0.9192085
## IUM83_06247 IUM83_13363 IUM83_01500 IUM83_18867 IUM83_16653
## 0.9191978 0.9189395 0.9188151 0.9187672 0.9187597
## IUM83_17867 IUM83_11782 IUM83_07885 IUM83_14865 TanjilG_14704
## 0.9187467 0.9187137 0.9187031 0.9186887 0.9184336
## IUM83_10036 TanjilG_07693 IUM83_07104 IUM83_12977 IUM83_09641
## 0.9183413 0.9180261 0.9178683 0.9176916 0.9175569
## IUM83_09778 IUM83_00544 IUM83_12206 IUM83_03767 IUM83_15163
## 0.9173800 0.9170256 0.9169878 0.9169852 0.9166366
## IUM83_10793 IUM83_07854 IUM83_10728 IUM83_00506 IUM83_02538
## 0.9161525 0.9161027 0.9156274 0.9154646 0.9153035
## IUM83_00295 IUM83_05187 IUM83_08927 IUM83_10703 TanjilG_28077
## 0.9151191 0.9150125 0.9149116 0.9147859 0.9147738
## IUM83_03638 IUM83_07557 IUM83_15218 IUM83_09173 TanjilG_22875
## 0.9146903 0.9144889 0.9142965 0.9140784 0.9139642
## IUM83_19691 IUM83_15611 IUM83_15866 IUM83_19948 IUM83_15042
## 0.9139635 0.9137856 0.9135157 0.9132586 0.9128842
## TanjilG_05873 IUM83_05860 IUM83_05664 IUM83_05474 IUM83_08745
## 0.9127386 0.9127286 0.9125253 0.9125143 0.9125090
## IUM83_14702 IUM83_10623 IUM83_13369 IUM83_03677 IUM83_14058
## 0.9124160 0.9119877 0.9115551 0.9113478 0.9113276
## IUM83_16691 IUM83_15365 IUM83_07672 IUM83_00817 TanjilG_26190
## 0.9111657 0.9111056 0.9109796 0.9109547 0.9109056
## IUM83_07853 IUM83_13425 IUM83_16673 IUM83_10374 IUM83_18403
## 0.9107862 0.9106955 0.9106161 0.9105688 0.9105064
## IUM83_03462 IUM83_06943 IUM83_02162 IUM83_18562 TanjilG_28036
## 0.9103118 0.9103025 0.9102912 0.9102568 0.9101162
## IUM83_02762 IUM83_12120 IUM83_17208 IUM83_09399 IUM83_16168
## 0.9097666 0.9097435 0.9096110 0.9094530 0.9093950
## IUM83_10239 TanjilG_07908 IUM83_15388 IUM83_11674 IUM83_18836
## 0.9093728 0.9093578 0.9092473 0.9088043 0.9087523
## IUM83_12327 IUM83_06375 IUM83_03001 IUM83_04167 IUM83_12645
## 0.9087323 0.9087224 0.9087031 0.9085646 0.9085223
## IUM83_01595 IUM83_04764 IUM83_03602 IUM83_17275 IUM83_14302
## 0.9084798 0.9084283 0.9082112 0.9080783 0.9079166
## TanjilG_27771 IUM83_13205 IUM83_00226 IUM83_06742 IUM83_14774
## 0.9076940 0.9076069 0.9072552 0.9072107 0.9071101
## IUM83_12300 IUM83_10314 IUM83_17311 IUM83_03083 IUM83_00168
## 0.9070388 0.9069308 0.9069264 0.9064764 0.9064753
## IUM83_03770 IUM83_10304 IUM83_04376 IUM83_12598 TanjilG_18263
## 0.9062404 0.9062193 0.9062024 0.9061237 0.9060657
## IUM83_11880 IUM83_18642 IUM83_05004 IUM83_02427 IUM83_16764
## 0.9059775 0.9057410 0.9055792 0.9055413 0.9052958
## IUM83_08322 IUM83_16335 IUM83_07466 IUM83_13401 IUM83_00289
## 0.9051441 0.9051402 0.9048023 0.9047835 0.9045374
## IUM83_10291 IUM83_12593 IUM83_14988 IUM83_08699 IUM83_00804
## 0.9044915 0.9042828 0.9040939 0.9040734 0.9038068
## IUM83_08248 IUM83_00982 IUM83_11489 IUM83_09100 IUM83_02828
## 0.9036485 0.9033819 0.9032524 0.9031870 0.9030439
## IUM83_15576 IUM83_14743 IUM83_11936 IUM83_08996 IUM83_03897
## 0.9029419 0.9029071 0.9028776 0.9025794 0.9025152
## IUM83_08644 IUM83_02141 IUM83_07968 TanjilG_12971 IUM83_19079
## 0.9024289 0.9024280 0.9023698 0.9022649 0.9019793
## IUM83_16302 IUM83_15989 IUM83_17270 IUM83_10748 IUM83_16410
## 0.9019271 0.9016071 0.9015950 0.9014310 0.9012301
## IUM83_11709 IUM83_03143 IUM83_10197 IUM83_02502 IUM83_08520
## 0.9012103 0.9010372 0.9009203 0.9006073 0.9003414
## TanjilG_21316 IUM83_16239 IUM83_19682 IUM83_06223 IUM83_01792
## 0.9002675 0.9002449 0.8999715 0.8999272 0.8998489
## IUM83_15744 TanjilG_24326 IUM83_17023 IUM83_17407 IUM83_15818
## 0.8998365 0.8997111 0.8995990 0.8993928 0.8992252
## IUM83_10855 IUM83_18402 IUM83_17064 IUM83_09554 IUM83_03915
## 0.8991725 0.8991284 0.8990929 0.8988511 0.8988161
## IUM83_05819 IUM83_06621 IUM83_17279 IUM83_19137 IUM83_06936
## 0.8987106 0.8985143 0.8983678 0.8982952 0.8981878
## IUM83_04136 TanjilG_19120 IUM83_10371 TanjilG_28680 IUM83_19146
## 0.8980505 0.8980302 0.8980258 0.8976757 0.8976169
## TanjilG_22200 IUM83_09066 IUM83_07173 IUM83_05760 IUM83_16817
## 0.8976125 0.8974464 0.8974168 0.8972602 0.8972571
## IUM83_00362 IUM83_16534 IUM83_16771 IUM83_03474 IUM83_16085
## 0.8972537 0.8972400 0.8971451 0.8967141 0.8966921
## IUM83_03390 IUM83_06254 IUM83_13780 IUM83_09298 IUM83_17857
## 0.8966135 0.8965360 0.8963398 0.8960213 0.8958888
## IUM83_04191 IUM83_18987 IUM83_17144 IUM83_05328 TanjilG_06347
## 0.8958520 0.8955298 0.8955252 0.8954716 0.8954688
## IUM83_18502 IUM83_16257 IUM83_07766 IUM83_09182 TanjilG_24766
## 0.8953801 0.8953191 0.8951299 0.8950142 0.8947538
## IUM83_00909 IUM83_12708 IUM83_07638 IUM83_08675 IUM83_12993
## 0.8945883 0.8944019 0.8943053 0.8942349 0.8941855
## IUM83_00480 IUM83_11144 IUM83_15235 IUM83_16090 IUM83_08202
## 0.8939938 0.8939640 0.8936176 0.8934287 0.8932861
## IUM83_01132 IUM83_03367 IUM83_08246 TanjilG_18545 IUM83_14371
## 0.8929766 0.8928129 0.8927794 0.8927388 0.8927331
## IUM83_17143 IUM83_16088 TanjilG_06882 IUM83_13727 IUM83_01447
## 0.8925654 0.8923033 0.8922346 0.8921667 0.8920365
## IUM83_08197 IUM83_12423 IUM83_15395 IUM83_06881 IUM83_11822
## 0.8919037 0.8914204 0.8912823 0.8911479 0.8910433
## IUM83_00462 IUM83_12333 IUM83_19901 IUM83_04138 IUM83_11390
## 0.8909793 0.8909374 0.8908708 0.8906697 0.8906260
## IUM83_16408 IUM83_18989 TanjilG_01373 IUM83_05904 IUM83_09437
## 0.8905971 0.8904955 0.8904919 0.8900205 0.8899112
## IUM83_02142 IUM83_10415 IUM83_09475 IUM83_12810 IUM83_09873
## 0.8898953 0.8898583 0.8896462 0.8895353 0.8892878
## IUM83_12623 IUM83_12839 IUM83_04283 IUM83_18474 IUM83_12951
## 0.8890737 0.8890681 0.8888841 0.8888626 0.8888487
## IUM83_05940 IUM83_17687 IUM83_15267 IUM83_12657 IUM83_12108
## 0.8887003 0.8884319 0.8884053 0.8883214 0.8882238
## IUM83_12735 IUM83_13777 IUM83_06802 TanjilG_06537 IUM83_03522
## 0.8881824 0.8881251 0.8881230 0.8880549 0.8880480
## IUM83_06370 TanjilG_23176 IUM83_08803 IUM83_00924 IUM83_06743
## 0.8880153 0.8879923 0.8878632 0.8874463 0.8874374
## IUM83_00705 IUM83_19695 TanjilG_31893 IUM83_00404 IUM83_08450
## 0.8873094 0.8871842 0.8871662 0.8869721 0.8869689
## IUM83_07384 IUM83_00424 TanjilG_10469 IUM83_16054 IUM83_03285
## 0.8868287 0.8868285 0.8866428 0.8863613 0.8861641
## IUM83_00108 IUM83_15400 IUM83_14340 IUM83_07652 IUM83_00735
## 0.8861476 0.8859956 0.8857853 0.8857038 0.8856574
## IUM83_04271 IUM83_01604 IUM83_15221 IUM83_06674 TanjilG_22505
## 0.8855966 0.8855535 0.8855186 0.8854611 0.8854025
## IUM83_17301 IUM83_14003 TanjilG_02278 IUM83_01066 IUM83_04418
## 0.8852313 0.8850379 0.8850195 0.8848133 0.8847485
## IUM83_05183 IUM83_12493 TanjilG_17582 IUM83_14255 IUM83_03455
## 0.8845684 0.8844777 0.8841635 0.8841602 0.8841541
## IUM83_04267 IUM83_02508 IUM83_02192 IUM83_03527 IUM83_18766
## 0.8841127 0.8841073 0.8840899 0.8840578 0.8838840
## IUM83_13410 TanjilG_03083 IUM83_11245 IUM83_08991 IUM83_08672
## 0.8838243 0.8836233 0.8835213 0.8833186 0.8832271
## IUM83_08032 IUM83_16837 IUM83_08707 IUM83_06817 IUM83_08626
## 0.8831629 0.8831050 0.8830127 0.8828163 0.8828136
## IUM83_15721 IUM83_02388 IUM83_15292 IUM83_02951 IUM83_18072
## 0.8827739 0.8826113 0.8824468 0.8824018 0.8822345
## IUM83_09342 IUM83_17765 IUM83_12201 IUM83_10365 IUM83_03577
## 0.8821441 0.8820465 0.8819696 0.8819503 0.8818464
## IUM83_18507 IUM83_04498 IUM83_01404 TanjilG_02984 IUM83_09020
## 0.8816930 0.8816682 0.8816158 0.8815173 0.8814846
## IUM83_01165 IUM83_18788 IUM83_06379 IUM83_11300 IUM83_19949
## 0.8814641 0.8814095 0.8813704 0.8812429 0.8811250
## IUM83_09786 IUM83_17733 TanjilG_22501 IUM83_02244 IUM83_07456
## 0.8811215 0.8808965 0.8805747 0.8805435 0.8804946
## IUM83_07918 TanjilG_13860 IUM83_18529 IUM83_01857 IUM83_07300
## 0.8803766 0.8803693 0.8802954 0.8802686 0.8799800
## IUM83_04643 IUM83_10551 IUM83_03005 IUM83_12634 IUM83_13627
## 0.8797598 0.8796381 0.8795721 0.8794986 0.8794228
## IUM83_12180 IUM83_04560 TanjilG_13477 IUM83_02943 TanjilG_28933
## 0.8792935 0.8792029 0.8790525 0.8788848 0.8787454
## TanjilG_03934 IUM83_12021 IUM83_04205 IUM83_14238 IUM83_01344
## 0.8783065 0.8782968 0.8782831 0.8782468 0.8781750
## IUM83_07332 IUM83_16336 TanjilG_12085 IUM83_12252 IUM83_07776
## 0.8780891 0.8780169 0.8779403 0.8778818 0.8775136
## IUM83_16815 IUM83_19044 IUM83_05921 IUM83_12883 IUM83_12436
## 0.8774963 0.8774866 0.8774105 0.8774045 0.8771392
## TanjilG_10862 IUM83_00841 IUM83_12607 IUM83_01211 IUM83_18413
## 0.8770408 0.8767799 0.8767543 0.8764890 0.8764817
## IUM83_04008 IUM83_18330 IUM83_02751 TanjilG_25565 IUM83_05650
## 0.8764529 0.8762614 0.8762472 0.8761075 0.8759587
## IUM83_03439 IUM83_12231 IUM83_18386 IUM83_19541 IUM83_06142
## 0.8758883 0.8758175 0.8756994 0.8756299 0.8755503
## IUM83_02246 IUM83_10233 IUM83_09962 IUM83_01307 TanjilG_07528
## 0.8755041 0.8753450 0.8751675 0.8751358 0.8749877
## IUM83_10766 IUM83_17475 IUM83_18038 IUM83_16533 IUM83_05645
## 0.8748720 0.8747692 0.8747277 0.8745669 0.8744377
## IUM83_07848 IUM83_08182 IUM83_00204 TanjilG_28673 IUM83_09912
## 0.8743687 0.8743474 0.8742551 0.8741380 0.8741167
## IUM83_15663 IUM83_10280 IUM83_16702 IUM83_08242 IUM83_14724
## 0.8739145 0.8737059 0.8736158 0.8735152 0.8734241
## IUM83_05871 IUM83_03424 IUM83_01966 IUM83_04597 IUM83_08329
## 0.8733995 0.8731955 0.8729917 0.8729179 0.8728516
## IUM83_06848 IUM83_18228 IUM83_18340 IUM83_13285 IUM83_09389
## 0.8728255 0.8728239 0.8728070 0.8726376 0.8726117
## IUM83_03149 IUM83_05911 TanjilG_17557 IUM83_03210 IUM83_06105
## 0.8724469 0.8724451 0.8723199 0.8722161 0.8717340
## IUM83_13860 IUM83_15604 IUM83_12219 IUM83_00645 TanjilG_17458
## 0.8717087 0.8714839 0.8713050 0.8711553 0.8710068
## IUM83_06453 IUM83_01174 IUM83_08251 IUM83_16095 IUM83_07413
## 0.8709907 0.8708836 0.8706892 0.8706097 0.8704063
## IUM83_16873 IUM83_12025 IUM83_01188 IUM83_15882 IUM83_15703
## 0.8703169 0.8700674 0.8700499 0.8700257 0.8697153
## IUM83_00780 IUM83_11014 IUM83_09803 IUM83_07829 IUM83_14593
## 0.8695522 0.8693685 0.8693363 0.8692765 0.8691441
## IUM83_14885 IUM83_02873 IUM83_09058 IUM83_16618 IUM83_00622
## 0.8690989 0.8690320 0.8690032 0.8689747 0.8689585
## IUM83_06244 IUM83_05747 IUM83_08217 IUM83_02307 IUM83_17084
## 0.8688177 0.8687383 0.8686577 0.8686373 0.8686286
## IUM83_13877 IUM83_09407 TanjilG_15399 IUM83_18480 IUM83_03520
## 0.8686213 0.8686048 0.8685575 0.8682601 0.8682498
## IUM83_18647 IUM83_16091 IUM83_17466 IUM83_04915 TanjilG_25004
## 0.8681053 0.8679664 0.8678496 0.8678165 0.8678026
## TanjilG_27391 IUM83_06579 IUM83_12350 IUM83_03914 IUM83_08683
## 0.8676357 0.8675422 0.8674843 0.8669509 0.8669486
## IUM83_08664 IUM83_02451 IUM83_04173 IUM83_00528 IUM83_19306
## 0.8668934 0.8668081 0.8667480 0.8661935 0.8661567
## IUM83_02720 IUM83_16805 IUM83_01420 IUM83_14714 IUM83_04982
## 0.8657495 0.8657129 0.8654092 0.8653371 0.8653224
## IUM83_18908 IUM83_14267 TanjilG_06126 IUM83_11916 IUM83_02570
## 0.8651453 0.8651412 0.8650951 0.8647870 0.8645572
## TanjilG_32729 IUM83_00233 IUM83_12469 IUM83_09607 IUM83_10241
## 0.8642798 0.8642527 0.8642239 0.8641807 0.8641719
## IUM83_08316 IUM83_00262 IUM83_17308 TanjilG_32842 IUM83_00632
## 0.8640698 0.8638388 0.8638151 0.8637510 0.8636577
## IUM83_03038 IUM83_11748 IUM83_09270 IUM83_18208 IUM83_00488
## 0.8634965 0.8634027 0.8633375 0.8632668 0.8632646
## IUM83_05338 IUM83_08363 IUM83_06015 IUM83_01206 IUM83_13654
## 0.8632170 0.8631349 0.8631213 0.8630807 0.8630671
## IUM83_10486 IUM83_04325 IUM83_06850 IUM83_07933 IUM83_06984
## 0.8628844 0.8628457 0.8627595 0.8627198 0.8624689
## IUM83_19669 IUM83_08910 IUM83_14416 IUM83_06807 IUM83_06068
## 0.8624090 0.8622928 0.8620955 0.8620866 0.8615652
## IUM83_03811 IUM83_04627 IUM83_09245 IUM83_07210 TanjilG_29402
## 0.8614389 0.8610382 0.8607432 0.8606709 0.8606229
## TanjilG_31006 IUM83_06026 IUM83_10568 TanjilG_06203 IUM83_01384
## 0.8606106 0.8604317 0.8603663 0.8602362 0.8602061
## IUM83_17411 IUM83_05545 IUM83_08849 TanjilG_05899 IUM83_00590
## 0.8593547 0.8593465 0.8591673 0.8591008 0.8589317
## IUM83_03953 IUM83_10773 IUM83_09410 IUM83_16270 IUM83_00731
## 0.8589023 0.8588695 0.8588488 0.8588019 0.8587099
## IUM83_08537 TanjilG_07123 IUM83_17946 TanjilG_24182 IUM83_04059
## 0.8586943 0.8586879 0.8585121 0.8584546 0.8583871
## IUM83_00274 IUM83_10905 IUM83_16107 IUM83_13463 IUM83_03047
## 0.8583487 0.8581815 0.8581551 0.8579791 0.8579284
## IUM83_01843 IUM83_11426 IUM83_02110 IUM83_02718 IUM83_09997
## 0.8578983 0.8577976 0.8577837 0.8577247 0.8576322
## IUM83_01642 IUM83_18527 IUM83_02139 IUM83_18051 IUM83_17272
## 0.8575219 0.8574485 0.8574297 0.8573800 0.8573753
## IUM83_00157 IUM83_13745 IUM83_00172 IUM83_04932 TanjilG_22017
## 0.8573246 0.8572763 0.8572751 0.8572495 0.8571897
## IUM83_19293 IUM83_16729 IUM83_06784 IUM83_08234 IUM83_03578
## 0.8569665 0.8569629 0.8569388 0.8568397 0.8567783
## IUM83_02121 TanjilG_32644 IUM83_18536 IUM83_02872 IUM83_11424
## 0.8565579 0.8565268 0.8565138 0.8564508 0.8564298
## IUM83_08759 IUM83_05232 TanjilG_07562 IUM83_01235 IUM83_13530
## 0.8563508 0.8562846 0.8560813 0.8560804 0.8560465
## IUM83_19978 TanjilG_23810 IUM83_00547 IUM83_17517 IUM83_03409
## 0.8557193 0.8556129 0.8555142 0.8553762 0.8550729
## IUM83_10949 IUM83_06725 IUM83_13978 IUM83_16094 TanjilG_33051
## 0.8550383 0.8549851 0.8547290 0.8545871 0.8545599
## IUM83_05567 IUM83_04503 IUM83_04523 TanjilG_26827 IUM83_16719
## 0.8545226 0.8539282 0.8536599 0.8535198 0.8534239
## IUM83_01295 IUM83_04687 IUM83_13672 IUM83_02624 IUM83_01718
## 0.8533031 0.8532924 0.8530867 0.8529128 0.8528901
## IUM83_00535 TanjilG_18559 IUM83_07690 IUM83_18699 IUM83_07124
## 0.8528369 0.8527995 0.8527014 0.8526713 0.8523635
## TanjilG_23456 IUM83_01208 IUM83_03046 IUM83_14076 IUM83_19452
## 0.8519811 0.8519771 0.8519646 0.8518781 0.8518565
## IUM83_05383 IUM83_08774 TanjilG_01306 IUM83_09230 IUM83_00942
## 0.8518521 0.8518436 0.8513695 0.8513515 0.8513315
## IUM83_08931 TanjilG_28083 IUM83_06832 IUM83_06934 IUM83_19678
## 0.8510495 0.8510461 0.8508847 0.8506744 0.8506718
## TanjilG_08743 IUM83_01028 IUM83_14222 IUM83_00127 IUM83_10215
## 0.8505542 0.8505481 0.8504783 0.8504571 0.8504259
## IUM83_14973 IUM83_11676 IUM83_03523 IUM83_09222 IUM83_06066
## 0.8503873 0.8503233 0.8502711 0.8502613 0.8501287
## IUM83_05680 IUM83_06098 IUM83_13867 IUM83_05525 IUM83_13963
## 0.8499785 0.8499454 0.8499066 0.8496618 0.8494658
## TanjilG_09401 IUM83_04508 IUM83_09122 IUM83_03221 IUM83_06700
## 0.8494197 0.8493236 0.8492879 0.8492422 0.8490677
## IUM83_04421 TanjilG_04275 TanjilG_27388 IUM83_07401 IUM83_18994
## 0.8489684 0.8488806 0.8487886 0.8486181 0.8486150
## IUM83_00340 IUM83_11498 IUM83_17482 IUM83_01669 IUM83_02367
## 0.8481284 0.8479725 0.8479420 0.8478582 0.8475650
## TanjilG_04971 IUM83_14842 IUM83_04791 IUM83_17905 IUM83_13034
## 0.8470963 0.8470374 0.8469965 0.8469635 0.8465822
## IUM83_07260 IUM83_07735 IUM83_02105 IUM83_11727 IUM83_08437
## 0.8465685 0.8465015 0.8464942 0.8463462 0.8460772
## TanjilG_30052 IUM83_12675 TanjilG_05036 IUM83_17214 IUM83_19174
## 0.8458403 0.8457677 0.8456549 0.8455680 0.8455653
## IUM83_01690 IUM83_19257 IUM83_03292 IUM83_13076 IUM83_07710
## 0.8455571 0.8454470 0.8450634 0.8450087 0.8448705
## IUM83_02173 IUM83_10461 IUM83_05956 IUM83_01934 IUM83_13729
## 0.8448144 0.8448012 0.8446203 0.8445763 0.8440950
## IUM83_10746 IUM83_19386 IUM83_08632 IUM83_01053 TanjilG_06246
## 0.8440396 0.8439865 0.8439703 0.8439348 0.8439248
## IUM83_08781 IUM83_10076 IUM83_01193 IUM83_12134 IUM83_05770
## 0.8438684 0.8438276 0.8437493 0.8436859 0.8434383
## IUM83_00387 IUM83_15476 IUM83_12985 IUM83_19349 IUM83_10867
## 0.8434334 0.8431255 0.8431094 0.8430864 0.8428466
## IUM83_00977 IUM83_10068 IUM83_17291 TanjilG_00301 TanjilG_24669
## 0.8427684 0.8426876 0.8425841 0.8424357 0.8423902
## IUM83_14546 IUM83_07388 IUM83_06899 IUM83_10010 IUM83_02448
## 0.8422904 0.8422873 0.8421991 0.8421549 0.8421459
## IUM83_01502 IUM83_04104 IUM83_09661 IUM83_12676 IUM83_06233
## 0.8421231 0.8418947 0.8418608 0.8417673 0.8417042
## IUM83_11065 IUM83_05203 IUM83_05537 IUM83_11811 IUM83_04490
## 0.8416014 0.8412875 0.8411431 0.8410653 0.8409184
## IUM83_19267 IUM83_04482 IUM83_04913 IUM83_18458 IUM83_07708
## 0.8408804 0.8408613 0.8407146 0.8406243 0.8404510
## IUM83_15205 IUM83_06020 IUM83_09709 IUM83_19003 IUM83_00253
## 0.8402686 0.8402331 0.8400515 0.8397513 0.8397199
## IUM83_13603 IUM83_09442 IUM83_01097 IUM83_03164 IUM83_10670
## 0.8397128 0.8396990 0.8396959 0.8396639 0.8396462
## IUM83_08016 TanjilG_09735 IUM83_04452 IUM83_05135 IUM83_11673
## 0.8393861 0.8393778 0.8392204 0.8389811 0.8388650
## IUM83_14931 IUM83_04108 IUM83_04469 IUM83_00550 IUM83_03657
## 0.8384491 0.8383660 0.8383470 0.8382203 0.8382202
## IUM83_09875 IUM83_06320 IUM83_19262 IUM83_04929 IUM83_01291
## 0.8382175 0.8381246 0.8380313 0.8379329 0.8379057
## IUM83_05047 IUM83_11522 IUM83_09452 IUM83_02732 IUM83_15494
## 0.8377923 0.8377526 0.8376561 0.8376354 0.8376009
## IUM83_05391 IUM83_07930 IUM83_15147 IUM83_07379 IUM83_01496
## 0.8372071 0.8370311 0.8369107 0.8366372 0.8366165
## IUM83_14066 IUM83_07691 IUM83_10049 IUM83_16080 TanjilG_10223
## 0.8365302 0.8364943 0.8364347 0.8363825 0.8363233
## IUM83_08279 TanjilG_31531 TanjilG_14771 IUM83_02705 TanjilG_30753
## 0.8361411 0.8357684 0.8354163 0.8353937 0.8352922
## TanjilG_13564 TanjilG_18552 IUM83_16152 IUM83_08676 IUM83_07951
## 0.8352774 0.8352289 0.8351620 0.8350356 0.8349146
## TanjilG_00593 IUM83_14403 TanjilG_09486 IUM83_15904 IUM83_02099
## 0.8348637 0.8345884 0.8345408 0.8344451 0.8343356
## IUM83_04841 IUM83_15164 IUM83_07991 IUM83_12982 IUM83_06510
## 0.8341384 0.8341113 0.8340494 0.8340444 0.8338583
## IUM83_19388 IUM83_15204 TanjilG_26340 IUM83_02311 IUM83_09998
## 0.8338218 0.8337551 0.8336875 0.8336858 0.8334429
## IUM83_05103 TanjilG_21090 IUM83_12505 IUM83_16212 IUM83_04536
## 0.8334263 0.8333534 0.8332614 0.8331763 0.8330108
## IUM83_18550 IUM83_09385 IUM83_04293 IUM83_16932 IUM83_12539
## 0.8329824 0.8327744 0.8326300 0.8326219 0.8325216
## TanjilG_12741 IUM83_01795 IUM83_19420 IUM83_14313 IUM83_18140
## 0.8321542 0.8317897 0.8317834 0.8317692 0.8316388
## IUM83_04133 IUM83_10870 IUM83_10938 IUM83_16482 IUM83_08114
## 0.8313257 0.8312520 0.8311864 0.8311543 0.8311356
## IUM83_07070 IUM83_00270 IUM83_09756 TanjilG_02261 IUM83_12628
## 0.8311044 0.8310204 0.8303372 0.8301888 0.8301584
## IUM83_13632 IUM83_10529 IUM83_02374 IUM83_08391 IUM83_17861
## 0.8298491 0.8298186 0.8297848 0.8295145 0.8294832
## IUM83_15907 TanjilG_10629 IUM83_03284 TanjilG_30685 IUM83_01437
## 0.8294676 0.8294538 0.8294177 0.8292220 0.8291305
## IUM83_15927 IUM83_14193 TanjilG_24744 IUM83_01830 IUM83_10086
## 0.8287168 0.8286494 0.8285652 0.8285605 0.8283978
## IUM83_18349 IUM83_16664 IUM83_04760 TanjilG_24786 IUM83_08225
## 0.8283438 0.8281726 0.8277885 0.8277692 0.8276411
## IUM83_14794 IUM83_10906 IUM83_05673 TanjilG_11271 IUM83_04621
## 0.8273710 0.8272801 0.8271923 0.8271774 0.8271327
## IUM83_06078 IUM83_12679 IUM83_01037 IUM83_08281 IUM83_00957
## 0.8271022 0.8270136 0.8269241 0.8269058 0.8268822
## IUM83_07147 IUM83_17727 IUM83_10316 TanjilG_12875 IUM83_09349
## 0.8267961 0.8266913 0.8264399 0.8264344 0.8263834
## TanjilG_22092 IUM83_06847 TanjilG_10461 TanjilG_02798 TanjilG_00097
## 0.8261288 0.8260686 0.8259796 0.8258629 0.8257172
## IUM83_18469 IUM83_05838 IUM83_04065 IUM83_12138 IUM83_06462
## 0.8253571 0.8250295 0.8249794 0.8249069 0.8247093
## IUM83_15356 IUM83_00623 IUM83_12501 IUM83_13019 IUM83_00034
## 0.8246637 0.8246241 0.8245113 0.8240822 0.8239395
## IUM83_01684 IUM83_07767 IUM83_17284 IUM83_04666 IUM83_15460
## 0.8238998 0.8235483 0.8234856 0.8233414 0.8232764
## IUM83_17391 IUM83_15319 TanjilG_24731 TanjilG_13117 TanjilG_17611
## 0.8231721 0.8230196 0.8229594 0.8229003 0.8227386
## IUM83_05837 IUM83_04570 IUM83_04856 IUM83_11430 IUM83_06643
## 0.8227037 0.8226645 0.8226586 0.8226166 0.8225940
## IUM83_00883 TanjilG_25691 IUM83_01675 IUM83_07053 IUM83_03150
## 0.8225548 0.8223544 0.8223449 0.8222936 0.8219298
## TanjilG_03933 TanjilG_15707 IUM83_02717 IUM83_01663 IUM83_08172
## 0.8218641 0.8217772 0.8216875 0.8214419 0.8212496
## IUM83_06519 IUM83_12238 IUM83_04068 IUM83_10879 IUM83_04601
## 0.8211844 0.8210197 0.8205626 0.8205407 0.8205407
## IUM83_17812 IUM83_13667 TanjilG_11069 IUM83_16322 IUM83_16207
## 0.8203997 0.8203974 0.8203856 0.8202658 0.8199944
## IUM83_16458 IUM83_14181 TanjilG_32225 IUM83_14901 IUM83_08912
## 0.8199754 0.8199737 0.8199048 0.8198524 0.8198355
## TanjilG_04047 IUM83_06428 IUM83_13859 TanjilG_24049 IUM83_09204
## 0.8197111 0.8195847 0.8195464 0.8194762 0.8194462
## IUM83_01569 IUM83_19769 IUM83_18216 IUM83_15416 IUM83_05901
## 0.8192651 0.8192307 0.8191599 0.8191123 0.8190138
## TanjilG_16615 IUM83_08766 IUM83_04429 IUM83_11266 IUM83_01041
## 0.8188396 0.8188122 0.8182653 0.8182504 0.8181043
## IUM83_06469 IUM83_09996 IUM83_09163 IUM83_03558 IUM83_17261
## 0.8180510 0.8180312 0.8179954 0.8179490 0.8177510
## TanjilG_21655 TanjilG_30673 IUM83_07949 IUM83_00237 TanjilG_15111
## 0.8175792 0.8175731 0.8175014 0.8172623 0.8172548
## IUM83_13966 IUM83_16993 IUM83_08193 IUM83_07387 IUM83_09453
## 0.8172105 0.8171644 0.8171077 0.8167338 0.8167306
## IUM83_04568 IUM83_08044 IUM83_05038 TanjilG_04385 IUM83_10836
## 0.8166548 0.8165258 0.8164937 0.8163747 0.8162119
## TanjilG_06128 IUM83_03604 TanjilG_19917 IUM83_01034 IUM83_06612
## 0.8160517 0.8160477 0.8160064 0.8158986 0.8156968
## IUM83_13292 IUM83_05349 IUM83_01524 IUM83_15935 IUM83_10909
## 0.8156684 0.8155222 0.8155083 0.8154151 0.8153951
## IUM83_16286 IUM83_16675 IUM83_11629 IUM83_18816 IUM83_11871
## 0.8153088 0.8152893 0.8152368 0.8151996 0.8150394
## IUM83_19248 IUM83_03194 TanjilG_16897 IUM83_13977 IUM83_18023
## 0.8149158 0.8148788 0.8148603 0.8148210 0.8147738
## IUM83_11332 IUM83_08949 IUM83_09729 IUM83_03003 IUM83_00134
## 0.8145490 0.8145475 0.8144771 0.8144390 0.8143330
## IUM83_14580 IUM83_07116 TanjilG_30318 TanjilG_10670 IUM83_00712
## 0.8142224 0.8140871 0.8140549 0.8138396 0.8138309
## IUM83_18880 IUM83_03865 IUM83_08960 IUM83_01141 IUM83_06391
## 0.8136138 0.8136122 0.8135464 0.8135012 0.8134722
## IUM83_08381 IUM83_04737 IUM83_15618 IUM83_17622 TanjilG_07857
## 0.8133801 0.8133542 0.8132881 0.8132261 0.8131620
## IUM83_15596 IUM83_10674 IUM83_01436 IUM83_09639 IUM83_08167
## 0.8128202 0.8124390 0.8120467 0.8120183 0.8119693
## IUM83_00864 TanjilG_21382 IUM83_03489 IUM83_06321 IUM83_05676
## 0.8119653 0.8119397 0.8116872 0.8116246 0.8113276
## TanjilG_08235 TanjilG_07520 TanjilG_32419 IUM83_13440 IUM83_10569
## 0.8113133 0.8113108 0.8112945 0.8110606 0.8107642
## TanjilG_07788 IUM83_05431 TanjilG_05613 TanjilG_25532 IUM83_03356
## 0.8106301 0.8105531 0.8104993 0.8104612 0.8103903
## TanjilG_28093 IUM83_13701 TanjilG_15721 IUM83_15607 IUM83_15165
## 0.8103614 0.8102888 0.8100087 0.8098781 0.8098328
## IUM83_06910 IUM83_00657 TanjilG_22856 IUM83_10518 IUM83_06003
## 0.8096485 0.8095277 0.8095157 0.8093936 0.8093703
## IUM83_04859 IUM83_06660 IUM83_06792 IUM83_18088 TanjilG_03276
## 0.8089293 0.8088214 0.8085535 0.8085311 0.8082066
## IUM83_17987 IUM83_14704 IUM83_01886 IUM83_05094 IUM83_18965
## 0.8080448 0.8079788 0.8077586 0.8076682 0.8070156
## TanjilG_31589 IUM83_11615 TanjilG_08690 IUM83_14176 IUM83_00644
## 0.8069209 0.8068128 0.8067806 0.8067314 0.8065174
## IUM83_00403 IUM83_17455 IUM83_07465 IUM83_07700 TanjilG_27241
## 0.8065138 0.8064778 0.8064131 0.8062120 0.8060794
## IUM83_04595 IUM83_00911 IUM83_09507 IUM83_02831 IUM83_04819
## 0.8058228 0.8057348 0.8056446 0.8055515 0.8055280
## TanjilG_28326 IUM83_05813 IUM83_08284 TanjilG_32407 IUM83_12699
## 0.8053925 0.8052052 0.8051538 0.8050542 0.8049432
## IUM83_07262 IUM83_11586 IUM83_17479 IUM83_19902 IUM83_13945
## 0.8049364 0.8048540 0.8046797 0.8044933 0.8044226
## TanjilG_17787 IUM83_09967 IUM83_15030 IUM83_07148 TanjilG_32528
## 0.8044034 0.8039909 0.8038994 0.8038734 0.8037431
## IUM83_04950 IUM83_12949 IUM83_08976 TanjilG_28128 IUM83_01695
## 0.8034808 0.8034158 0.8033151 0.8033138 0.8031980
## IUM83_06734 IUM83_17762 IUM83_07828 TanjilG_01045 IUM83_14908
## 0.8024527 0.8022681 0.8022406 0.8020020 0.8019299
## IUM83_09596 IUM83_07349 TanjilG_31433 IUM83_08522 IUM83_02349
## 0.8014356 0.8014103 0.8013338 0.8012781 0.8012672
## IUM83_14366 IUM83_07855 IUM83_00317 IUM83_11633 IUM83_00661
## 0.8011792 0.8011628 0.8011512 0.8010479 0.8010013
## IUM83_14881 IUM83_06736 IUM83_16661 IUM83_16667 IUM83_05372
## 0.8009024 0.8007441 0.8006172 0.8004711 0.8004211
## TanjilG_19204 IUM83_01826
## 0.8002740 0.8000830
res <- lapply(X=1:length(IUM83RxLR),FUN=corselect)
str(res)
## List of 16
## $ : Named num [1:1607] 1 0.985 0.981 0.981 0.98 ...
## ..- attr(*, "names")= chr [1:1607] "IUM83_01938" "IUM83_16697" "IUM83_17796" "IUM83_19033" ...
## $ : Named num [1:1392] 1 0.998 0.998 0.995 0.995 ...
## ..- attr(*, "names")= chr [1:1392] "IUM83_01936" "IUM83_05384" "IUM83_09517" "IUM83_00797" ...
## $ : Named num [1:375] 1 0.981 0.975 0.975 0.973 ...
## ..- attr(*, "names")= chr [1:375] "IUM83_10648" "TanjilG_30020" "IUM83_16797" "IUM83_17036" ...
## $ : Named num [1:295] 1 0.989 0.981 0.979 0.976 ...
## ..- attr(*, "names")= chr [1:295] "IUM83_03493" "IUM83_09012" "IUM83_04033" "TanjilG_30040" ...
## $ : Named num [1:1862] 1 0.991 0.991 0.989 0.988 ...
## ..- attr(*, "names")= chr [1:1862] "IUM83_04400" "TanjilG_08717" "TanjilG_06642" "TanjilG_21259" ...
## $ : Named num [1:181] 1 0.98 0.98 0.973 0.972 ...
## ..- attr(*, "names")= chr [1:181] "IUM83_18785" "IUM83_09046" "IUM83_09012" "TanjilG_24851" ...
## $ : Named num [1:1420] 1 0.988 0.988 0.986 0.986 ...
## ..- attr(*, "names")= chr [1:1420] "IUM83_04885" "TanjilG_01995" "IUM83_00409" "TanjilG_15908" ...
## $ : Named num [1:590] 1 0.966 0.963 0.962 0.96 ...
## ..- attr(*, "names")= chr [1:590] "IUM83_08873" "TanjilG_21624" "IUM83_04385" "TanjilG_30382" ...
## $ : Named num [1:2314] 1 0.986 0.986 0.985 0.985 ...
## ..- attr(*, "names")= chr [1:2314] "IUM83_18765" "IUM83_14313" "IUM83_16664" "IUM83_17278" ...
## $ : Named num [1:2392] 1 0.999 0.998 0.998 0.998 ...
## ..- attr(*, "names")= chr [1:2392] "IUM83_11727" "IUM83_09385" "IUM83_18647" "IUM83_09230" ...
## $ : Named num [1:2229] 1 0.999 0.998 0.998 0.998 ...
## ..- attr(*, "names")= chr [1:2229] "IUM83_05533" "IUM83_17288" "IUM83_19207" "IUM83_07789" ...
## $ : Named num [1:1283] 1 0.991 0.989 0.986 0.98 ...
## ..- attr(*, "names")= chr [1:1283] "IUM83_01163" "IUM83_09429" "IUM83_08645" "IUM83_14477" ...
## $ : Named num [1:2149] 1 0.998 0.997 0.997 0.997 ...
## ..- attr(*, "names")= chr [1:2149] "IUM83_10036" "IUM83_01293" "IUM83_17407" "IUM83_12146" ...
## $ : Named num [1:2034] 1 0.992 0.991 0.99 0.99 ...
## ..- attr(*, "names")= chr [1:2034] "IUM83_19033" "IUM83_13015" "IUM83_05571" "IUM83_08530" ...
## $ : Named num [1:1960] 1 0.996 0.995 0.994 0.993 ...
## ..- attr(*, "names")= chr [1:1960] "IUM83_01444" "IUM83_10203" "IUM83_17775" "IUM83_05106" ...
## $ : Named num [1:2248] 1 0.996 0.996 0.996 0.995 ...
## ..- attr(*, "names")= chr [1:2248] "IUM83_14945" "IUM83_11043" "IUM83_10538" "IUM83_00479" ...
library(limma)
##
## Attaching package: 'limma'
## The following object is masked from 'package:DESeq2':
##
## plotMA
## The following object is masked from 'package:BiocGenerics':
##
## plotMA
plotMDS(rpm)
plotMDS(t(rpm))
Session info
sessionInfo()
## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
##
## locale:
## [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
## [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
## [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] limma_3.48.3 gplots_3.1.1
## [3] reshape2_1.4.4 data.table_1.14.2
## [5] DESeq2_1.32.0 SummarizedExperiment_1.22.0
## [7] Biobase_2.52.0 MatrixGenerics_1.4.3
## [9] matrixStats_0.61.0 GenomicRanges_1.44.0
## [11] GenomeInfoDb_1.28.4 IRanges_2.26.0
## [13] S4Vectors_0.30.2 BiocGenerics_0.38.0
## [15] WGCNA_1.70-3 fastcluster_1.2.3
## [17] dynamicTreeCut_1.63-1 forcats_0.5.1
## [19] stringr_1.4.0 dplyr_1.0.7
## [21] purrr_0.3.4 readr_2.1.1
## [23] tidyr_1.1.4 tibble_3.1.6
## [25] ggplot2_3.3.5 tidyverse_1.3.1
##
## loaded via a namespace (and not attached):
## [1] colorspace_2.0-2 ellipsis_0.3.2 htmlTable_2.4.0
## [4] XVector_0.32.0 base64enc_0.1-3 fs_1.5.2
## [7] rstudioapi_0.13 bit64_4.0.5 AnnotationDbi_1.54.1
## [10] fansi_1.0.0 lubridate_1.8.0 xml2_1.3.3
## [13] codetools_0.2-18 splines_4.1.2 doParallel_1.0.16
## [16] cachem_1.0.6 impute_1.66.0 geneplotter_1.70.0
## [19] knitr_1.37 Formula_1.2-4 jsonlite_1.7.2
## [22] annotate_1.70.0 broom_0.7.11 cluster_2.1.2
## [25] GO.db_3.13.0 dbplyr_2.1.1 png_0.1-7
## [28] compiler_4.1.2 httr_1.4.2 backports_1.4.1
## [31] assertthat_0.2.1 Matrix_1.4-0 fastmap_1.1.0
## [34] cli_3.1.0 htmltools_0.5.2 tools_4.1.2
## [37] gtable_0.3.0 glue_1.6.0 GenomeInfoDbData_1.2.6
## [40] Rcpp_1.0.7 cellranger_1.1.0 jquerylib_0.1.4
## [43] vctrs_0.3.8 Biostrings_2.60.2 preprocessCore_1.54.0
## [46] iterators_1.0.13 xfun_0.29 rvest_1.0.2
## [49] lifecycle_1.0.1 gtools_3.9.2 XML_3.99-0.8
## [52] zlibbioc_1.38.0 scales_1.1.1 hms_1.1.1
## [55] RColorBrewer_1.1-2 yaml_2.2.1 memoise_2.0.1
## [58] gridExtra_2.3 sass_0.4.0 rpart_4.1-15
## [61] latticeExtra_0.6-29 stringi_1.7.6 RSQLite_2.2.9
## [64] highr_0.9 genefilter_1.74.1 foreach_1.5.1
## [67] checkmate_2.0.0 caTools_1.18.2 BiocParallel_1.26.2
## [70] rlang_0.4.12 pkgconfig_2.0.3 bitops_1.0-7
## [73] evaluate_0.14 lattice_0.20-45 htmlwidgets_1.5.4
## [76] bit_4.0.4 tidyselect_1.1.1 plyr_1.8.6
## [79] magrittr_2.0.1 R6_2.5.1 generics_0.1.1
## [82] Hmisc_4.6-0 DelayedArray_0.18.0 DBI_1.1.2
## [85] pillar_1.6.4 haven_2.4.3 foreign_0.8-82
## [88] withr_2.4.3 survival_3.2-13 KEGGREST_1.32.0
## [91] RCurl_1.98-1.5 nnet_7.3-17 modelr_0.1.8
## [94] crayon_1.4.2 KernSmooth_2.23-20 utf8_1.2.2
## [97] tzdb_0.2.0 rmarkdown_2.11 jpeg_0.1-9
## [100] locfit_1.5-9.4 grid_4.1.2 readxl_1.3.1
## [103] blob_1.2.2 reprex_2.0.1 digest_0.6.29
## [106] xtable_1.8-4 munsell_0.5.0 bslib_0.3.1