library(tidyverse)
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library(WGCNA)
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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