OROSmerge.R

OROSmerge<-function(memo){
  file<-list.files(pattern="*pvalue.csv")
  dge<-read.csv(file[1])
  os<-read.csv(file[2])
  out<-merge(dge,os,by="X")
  
  pick<-subset(out,pval.random.x < 10^-2 & pval.random.y<0.05 & TE.fixed.x*(TE.fixed.y-1)>0)
  pick<-pick[order(pick$pval.random.x),]
  if(nrow(pick)>50){
    pick<-pick[1:50,]
  }
  
  dir.create("pick")
  # be careful to run it or else it will takes quite long time
  for(i in 1:nrow(pick)){
    x<-paste("cp *-",pick[i,1],"* ./pick",sep="")
    system(x)
  }
  # install.packages("CMplot")
  setwd("pick")
  system("cp ../*.csv ./")
  library("CMplot")
  ensg<-read.table("~/hpc/db/hg19/ENSG.hg19.bed")
  ensgrlt<-ensg[match(unlist(lapply(strsplit(as.character(out$X),"[.]"),function(x) x[1])),ensg[,5]),]
  output<-data.frame(ensgrlt,out)
  
  chr2num<-function(x){
    x<-output$V1
    x<-gsub("chr","",x)
    x[x=="X"]<-23
    x[x=="Y"]<-24
    return(x)
  }
  
  write.csv(out,file=paste(memo,".tcga.pancancer.overall.rnaseq.dmg.smd.os.hr.csv",sep=""),quote=F)
  write.csv(pick,file=paste(memo,".tcga.pancancer.pick.rnaseq.dmg.smd.os.hr.csv",sep=""),quote=F)
  
  cminput<-na.omit(data.frame(SNP=output[,ncol(output)],Chromosome=chr2num(output$V1),Position=output$V2,trait1=output$pval.random.x,stringsAsFactors=F))
  CMplot(cminput,plot.type="b",memo=paste(memo,".dge.fix",sep=""),LOG10=TRUE,threshold=NULL,file="jpg",dpi=300,file.output=TRUE,verbose=TRUE,width=14,height=6)
  write.csv(cminput[order(cminput[,ncol(cminput)]),],file=paste(memo,".pval.manhattan.qqplot.meta.dge.bed",sep=""),quote=F,row.names=F)
  
  cminput<-na.omit(data.frame(SNP=output[,ncol(output)],Chromosome=chr2num(output$V1),Position=output$V2,trait1=output$pval.fix.y))
  CMplot(cminput,plot.type="b",memo=paste(memo,".os.fix",sep=""),LOG10=TRUE,threshold=NULL,file="jpg",dpi=300,file.output=TRUE,verbose=TRUE,width=14,height=6)
  write.csv(cminput[order(cminput[,ncol(cminput)]),],file=paste(memo,".pval.fix.manhattan.qqplot.meta.OS.HR.bed",sep=""),quote=F,row.names=F)
  
  cminput<-na.omit(data.frame(SNP=output[,ncol(output)],Chromosome=chr2num(output$V1),Position=output$V2,trait1=output$pval.random.y))
  CMplot(cminput,plot.type="b",memo=paste(memo,".os.random",sep=""),LOG10=TRUE,threshold=NULL,file="jpg",dpi=300,file.output=TRUE,verbose=TRUE,width=14,height=6)
  write.csv(cminput[order(cminput[,ncol(cminput)]),],file=paste(memo,".pval.random.manhattan.qqplot.meta.OS.HR.bed",sep=""),quote=F,row.names=F)
}