Mercurial > repos > ning > ebseq
view EBGeneTwoCondTest.R @ 25:b729d890413b draft
Uploaded
author | ning |
---|---|
date | Mon, 16 Jun 2014 12:31:02 -0400 |
parents | 696a1f7e23fd |
children |
line wrap: on
line source
sink(file="/tmp/none") sink("/dev/null") options(warn=-1) options(echo=F) invisible("EBSeq") suppressMessages(library("EBSeq")) args <- commandArgs(trailingOnly = T) inputfile <- args[1] WhetherSampleName <- args[2] CondIn <- args[3] FDR <- args[4] outputfile <- args[5] Sort.out<-args[6] Sort.out.FDR <-args[7] Sizesout <-args[8] Conditions=strsplit(CondIn,split=",")[[1]] if(WhetherSampleName=="y"){ ReadIn=read.table(inputfile,stringsAsFactors=F,header=T,sep="\t") Names=names(ReadIn)[-1] } if(WhetherSampleName=="n"){ ReadIn=read.table(inputfile,stringsAsFactors=F,header=F,sep="\t") Names=paste0("S",1:length(Conditions)) } if(class(ReadIn[[1]])=="character"){ GeneMat=do.call(cbind,ReadIn[-1]) rownames(GeneMat)=ReadIn[[1]] colnames(GeneMat)=Names } if(class(ReadIn[[1]])=="numeric"){ GeneMat=data.matrix(ReadIn) colnames(GeneMat)=Names } Sizes=MedianNorm(GeneMat) EBOut=EBTest(Data=GeneMat,Conditions=as.factor(Conditions),sizeFactors=Sizes, maxround=5) PP=GetPP(EBOut) PP.sort=sort(PP,decreasing=T) PP.sort.FDR=PP.sort[which(PP.sort>=1-as.numeric(FDR))] Data.norm=GetNormalizedMat(GeneMat, Sizes) FC=PostFC(EBOut) realFC=FC[[2]] postFC=FC[[1]] Mat=cbind(PP, realFC[names(PP)], postFC[names(PP)],Data.norm[names(PP),]) Mat.sort=cbind(PP.sort, realFC[names(PP.sort)], postFC[names(PP.sort)],Data.norm[names(PP.sort),]) if(length(PP.sort.FDR)>1)Mat.sort.FDR=cbind(PP.sort.FDR, realFC[names(PP.sort.FDR)], postFC[names(PP.sort.FDR)],Data.norm[names(PP.sort.FDR),]) if(length(PP.sort.FDR)==1)Mat.sort.FDR=matrix( c(PP.sort.FDR, realFC[names(PP.sort.FDR)], postFC[names(PP.sort.FDR)],Data.norm[names(PP.sort.FDR),]) ,nrow=1) colnames(Mat)=colnames(Mat.sort)= c("PPDE","RealFC","PosteriorFC",colnames(Data.norm)) if(length(PP.sort.FDR)>0)colnames(Mat.sort.FDR)= c("PPDE","RealFC","PosteriorFC",colnames(Data.norm)) write.table(round(Mat,2),file=outputfile,quote=F,col.names=T,row.names=T,sep = "\t") write.table(round(Mat.sort,2),file=Sort.out ,quote=F,col.names=T,row.names=T,sep = "\t") if(length(PP.sort.FDR)>0)write.table(round(Mat.sort.FDR,2),file=Sort.out.FDR,quote=F,col.names=T,row.names=T,sep = "\t") write.table(Sizes,file=Sizesout,quote=F,col.names=F,row.names=F,sep = "\t")