Commit earlier refactoring
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249
workflow/.old/apps/r/JoinInteractExps3dev.R
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249
workflow/.old/apps/r/JoinInteractExps3dev.R
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# JoinInteractExps3dev.R
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library(plyr)
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library(sos)
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library(dplyr)
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args <- commandArgs(TRUE)
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# Set output dir
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if (length(args) > 1) {
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outDir <- args[1]
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} else {
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outDir <- "./" # for legacy workflow
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}
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# Set sd value
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if (length(args) > 2) {
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sd <- args[2]
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} else {
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sd <- 2 # default value
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}
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# Set studyInfo file
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if (length(args) > 3) {
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studyInfo <- args[3]
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} else {
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studyInfo <- "../Code/StudyInfo.csv" # for legacy workflow
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}
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studies <- args[3:length(args)]
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# # Set SGDgeneList file path
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# if (length(args) > 3) {
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# SGDgeneList <- args[4]
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# } else {
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# SGDgeneList <- "../Code/SGD_features.tab" # for legacy workflow
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# }
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# if (length(args) > 4) {
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# outDir <- args[2]
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# } else {
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# outDir <- "/ZScores/" # for legacy workflow
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# }
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#The input files should be entered in order from the greatest number of rows(Orfs) to least.
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#Args <- commandArgs(TRUE)
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#if(length(Args)==0){
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# std=0
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#}else{
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# std=Args[1]
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#}
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print(paste("SD=",std))
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inputFiles <- c()
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for (study in 1:length(studies)) {
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zsFile <- file.path(study, 'zscores', 'zscores_interaction.csv')
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if (file.exists(zsFile)) {
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inputFiles[study] <- zsFile
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}
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}
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print(length(inputFiles)) #display the number of arguments on terminal
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# Read in the files for your experiment and
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# Join the two files at a time as a function of how many inputFile, list the larger file first ? in this example X2 has the larger number of genes.
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# If X1 has a larger number of genes, switch the order of X1 and X2
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if(length(inputFiles)==2) {
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X1 <- read.csv(file=inputFiles[1],stringsAsFactors = FALSE)
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X2 <- read.csv(file=inputFiles[2],stringsAsFactors = FALSE)
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X <- join(X1,X2,by="OrfRep")
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OBH=X[,order(colnames(X))] #OrderByHeader
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headSel= select(OBH, contains('OrfRep'), matches('Gene'), contains('Z_lm_K'), contains('Z_Shift_K'),contains('Z_lm_L'), contains('Z_Shift_L'))
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headSel= select(headSel, -'Gene.1') #remove 'Gene.1 column
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headSel2 = select(OBH, contains('OrfRep'), matches('Gene')) #Frame for interleaving Z_lm with Shift colums
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headSel2 = select(headSel2, -'Gene.1') #remove 'Gene.1 column #Frame for interleaving Z_lm with Shift colums
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}else if(length(inputFiles)==3){
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X1 <- read.csv(file=inputFiles[1],stringsAsFactors = FALSE) #exp1File,stringsAsFactors = FALSE)
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X2 <- read.csv(file=inputFiles[2],stringsAsFactors = FALSE) #exp2File,stringsAsFactors = FALSE)
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X3 <- read.csv(file=inputFiles[3],stringsAsFactors = FALSE) #exp3File,stringsAsFactors = FALSE)
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X <- join(X1,X2,by="OrfRep")
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X <- join(X,X3,by="OrfRep")
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OBH=X[,order(colnames(X))] #OrderByHeader
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headSel= select(OBH, contains('OrfRep'), matches('Gene'), contains('Z_lm_K'), contains('Z_Shift_K'),contains('Z_lm_L'), contains('Z_Shift_L'))
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headSel= select(headSel, -'Gene.1',-'Gene.2')
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headSel2 = select(OBH, contains('OrfRep'), matches('Gene'))
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headSel2 = select(headSel2, -'Gene.1',-'Gene.2')
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}else if(length(inputFiles)==4){
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X1 <- read.csv(file=inputFiles[1],stringsAsFactors = FALSE) #exp1File,stringsAsFactors = FALSE)
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X2 <- read.csv(file=inputFiles[2],stringsAsFactors = FALSE) #exp2File,stringsAsFactors = FALSE)
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X3 <- read.csv(file=inputFiles[3],stringsAsFactors = FALSE) #exp3File,stringsAsFactors = FALSE)
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X4 <- read.csv(file=inputFiles[4],stringsAsFactors = FALSE) #exp4File,stringsAsFactors = FALSE)
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X <- join(X1,X2,by="OrfRep")
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X <- join(X,X3,by="OrfRep")
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X <- join(X,X4,by="OrfRep")
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OBH=X[,order(colnames(X))] #OrderByHeader
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headSel= select(OBH, contains('OrfRep'), matches('Gene'), contains('Z_lm_K'), contains('Z_Shift_K'),contains('Z_lm_L'), contains('Z_Shift_L'))
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headSel= select(headSel, -'Gene.1',-'Gene.2',-'Gene.3')
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headSel2 = select(OBH, contains('OrfRep'), matches('Gene'))
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headSel2 = select(headSel2, -'Gene.1',-'Gene.2',-'Gene.3')
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}
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#headSel$contains('Z_Shift') %>% replace_na(0.001)
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headers<-colnames(headSel)
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i=0
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for(i in 1:length(headers)){
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if(grepl("Shift",headers[i])) {
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headSel[headers[i]][is.na(headSel[headers[i]])] = 0.001
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}
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if(grepl("Z_lm_",headers[i])) {
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headSel[headers[i]][is.na(headSel[headers[i]])] = 0.0001
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}
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}
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#2SD option code to exclude Z_lm values less than 2 standard Deviations
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REMcRdy= select(headSel, contains('OrfRep'), matches('Gene'), contains('Z_lm_'))
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shiftOnly= select(headSel, contains('OrfRep'), matches('Gene'), contains('Z_Shift'))
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# Code to replace the numeric (.1 .2 .3) headers with experiment names from StudyInfo.txt
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Labels <- read.csv(file= "../Code/StudyInfo.csv",stringsAsFactors = FALSE,sep= ",")
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# Using Text search grepl to relabel headers
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REMcRdyHdr= colnames(REMcRdy)
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REMcRdyLabels= 'asdf'
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shftHdr= colnames(shiftOnly)
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shiftLabels='asdf'
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shiftLabels[1:2]<-shftHdr[1:2]
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REMcRdyLabels[1:2]<-REMcRdyHdr[1:2]
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for(i in 3:(length(shftHdr))){
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if(i==3){
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shiftLabels[3]<-paste0(Labels[1,2],".",shftHdr[3])
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REMcRdyLabels[3]<-paste0(Labels[1,2],".",REMcRdyHdr[3]) }
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if(i==5){
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shiftLabels[5]<-paste0(Labels[1,2],".",shftHdr[5])
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REMcRdyLabels[5]<-paste0(Labels[1,2],".",REMcRdyHdr[5])
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}
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if(i==7){
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shiftLabels[7]<-paste0(Labels[1,2],".",shftHdr[7])
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REMcRdyLabels[7]<-paste0(Labels[1,2],".",REMcRdyHdr[7])
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}
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if(grepl(".1",shftHdr[i],fixed=true)){
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shiftLabels[i]<-paste0(Labels[2,2],".",shftHdr[i])
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REMcRdyLabels[i]<-paste0(Labels[2,2],".",REMcRdyHdr[i])}
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if (grepl(".2",shftHdr[i],fixed=true)){
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shiftLabels[i]<-paste0(Labels[3,2],".",shftHdr[i])
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REMcRdyLabels[i]<-paste0(Labels[3,2],".",REMcRdyHdr[i])}
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if(grepl(".3",shftHdr[i],fixed=true)){
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shiftLabels[i]<-paste0(Labels[4,2],".",shftHdr[i])
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REMcRdyLabels[i]<-paste0(Labels[4,2],".",REMcRdyHdr[i])}
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}
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for(i in 3:(length(REMcRdyLabels))){
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j=as.integer(i)
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REMcRdyLabels[j]<- gsub("[.]", "_", REMcRdyLabels[j])
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shiftLabels[j]<- gsub("[.]", "_", shiftLabels[j])
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}
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colnames(shiftOnly)<- shiftLabels
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colnames(REMcRdy)<- REMcRdyLabels
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combI=headSel2 #Starting Template orf, Genename columns
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# headersRemc<-colnames(REMcRdy)
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# Reorder columns to produce an interleaved set of Z_lm and Shift data for all the cpps.
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for(i in 3:length(colnames(REMcRdy))){
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combI=cbind.data.frame(combI, shiftOnly[i])
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combI=cbind.data.frame(combI, REMcRdy[i])
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}
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Vec1= NA
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Vec2= NA
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Vec3= NA
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Vec4= NA
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Vec5= NA
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Vec6= NA
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Vec7= NA
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Vec8= NA
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if(length(REMcRdy)==6){
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Vec1=abs(REMcRdy[,3])>=std
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Vec2=abs(REMcRdy[,4])>=std
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Vec3=abs(REMcRdy[,5])>=std
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Vec4=abs(REMcRdy[,6])>=std
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bolVec= Vec1 | Vec2 |Vec3 |Vec4
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REMcRdyGT2=REMcRdy[bolVec,1:2]
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REMcRdyGT2[ ,3:6]= REMcRdy[bolVec,3:6]
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shiftOnlyGT2=shiftOnly[bolVec,1:2]
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shiftOnlyGT2[ ,3:6]= shiftOnly[bolVec,3:6]
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}
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if(length(REMcRdy)==8){
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Vec1=abs(REMcRdy[,3])>=std
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Vec2=abs(REMcRdy[,4])>=std
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Vec3=abs(REMcRdy[,5])>=std
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Vec4=abs(REMcRdy[,6])>=std
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Vec5=abs(REMcRdy[,7])>=std
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Vec6=abs(REMcRdy[,8])>=std
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bolVec= Vec1 | Vec2 |Vec3 | Vec4 |Vec5 |Vec6
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REMcRdyGT2= REMcRdy[bolVec,1:2]
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REMcRdyGT2[ ,3:8]= REMcRdy[bolVec,3:8]
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shiftOnlyGT2= shiftOnly[bolVec,1:2]
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shiftOnlyGT2[ ,3:8]= shiftOnly[bolVec,3:8]
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}
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if(length(REMcRdy)==10){
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Vec1=abs(REMcRdy[,3])>=std
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Vec2=abs(REMcRdy[,4])>=std
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Vec3=abs(REMcRdy[,5])>=std
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Vec4=abs(REMcRdy[,6])>=std
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Vec5=abs(REMcRdy[,7])>=std
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Vec6=abs(REMcRdy[,8])>=std
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Vec7=abs(REMcRdy[,9])>=std
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Vec8=abs(REMcRdy[,10])>=std
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bolVec= Vec1 | Vec2 |Vec3 |Vec4|Vec5|Vec6|Vec7|Vec8
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REMcRdyGT2= REMcRdy[bolVec,1:2]
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REMcRdyGT2[ ,3:10]= REMcRdy[bolVec,3:10]
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shiftOnlyGT2= shiftOnly[bolVec,1:2]
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shiftOnlyGT2[ ,3:10]= shiftOnly[bolVec,3:10]
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}
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if(std!=0){
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REMcRdy= REMcRdyGT2 #[,2:length(REMcRdyGT2)]
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shiftOnly= shiftOnlyGT2 #[,2:length(shiftOnlyGT2)]
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}
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if(std==0){
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REMcRdy= REMcRdy #[,2:length(REMcRdy)]
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shiftOnly= shiftOnly #[,2:length(shiftOnly)]
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}
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# R places hidden "" around the header names. The following
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# is intended to remove those quote so that the "" do not blow up the Java REMc.
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# Use ,quote=F in the write.csv statement to fix R output file.
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#write.csv(combI,file = file.path(outDir,"CombinedKLzscores.csv"),row.names = FALSE)
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write.csv(REMcRdy,file=file.path(outDir,"REMcRdy_lm_only.csv"),row.names = FALSE, quote=F)
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write.csv(shiftOnly,file=file.path(outDir,"Shift_only.csv"),row.names = FALSE, quote=F)
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#LabelStd <- read.table(file= "./parameters.csv",stringsAsFactors = FALSE,sep= ",")
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LabelStd<- read.csv(file=studyInfo,stringsAsFactors = FALSE)
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print(std)
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LabelStd[,4]= as.numeric(std)
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write.csv(LabelStd,file=file.path(outDir,"parameters.csv"),row.names = FALSE)
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write.csv(LabelStd,file=studyInfo,row.names = FALSE)
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