Mercurial > repos > ning > ebseq
view EBGeneMultiCondTest.R @ 37:e11c511a2bb5 draft
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author | ning |
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date | Mon, 16 Jun 2014 16:23:31 -0400 |
parents | d049be55e5cf |
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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] PatternFile <- args[4] outputfile <- args[5] MAP.out<-args[6] Sizesout <-args[7] #write.table(PatternFile,outputfile,quote=F,col.names=T,row.names=T,sep = "\t") #write.table(args,outputfile,quote=F,col.names=T,row.names=T,sep = "\t") 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)) } #PatternIn=read.table(PatternFile,stringsAsFactors=F,header=T,sep="\t") PatternIn=read.table(PatternFile,stringsAsFactors=F,header=T,sep="\t",row.names=1) ##cms - changed on 11/15/13 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 } Patterns=data.matrix(PatternIn) Sizes=MedianNorm(GeneMat) EBOut=EBMultiTest(Data=GeneMat,Conditions=as.factor(Conditions), AllParti=Patterns,sizeFactors=Sizes, maxround=5) PPout=GetMultiPP(EBOut) MultiPP=PPout$PP MultiMAP=PPout$MAP Data.norm=round(GetNormalizedMat(GeneMat, Sizes),2) Mat=cbind(MultiMAP,Data.norm[names(MultiMAP),]) colnames(Mat)= c("MAP",Names) options(warn=-1) #write.table(round(MultiPP,2),file=outputfile,quote=F,col.names=T,row.names=T,sep = "\t") write.table(round(MultiPP,2),file=outputfile,quote=F,col.names=NA,row.names=T,sep = "\t") ##cms - changed on 11/15/13 #write.table(Mat,file=MAP.out ,quote=F,col.names=T,row.names=T,sep = "\t") write.table(Mat,file=MAP.out ,quote=F,col.names=NA,row.names=T,sep = "\t") ##cms - changed on 11/15/13 write.table(Sizes,file=Sizesout,quote=F,col.names=F,row.names=F,sep = "\t")