| Previous changeset 35:8b85a39cb625 (2014-06-16) Next changeset 37:e11c511a2bb5 (2014-06-16) |
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added:
EBIsoformMultiCondTest.R |
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| diff -r 8b85a39cb625 -r 7be90b1366d5 EBIsoformMultiCondTest.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/EBIsoformMultiCondTest.R Mon Jun 16 16:23:21 2014 -0400 |
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| @@ -0,0 +1,71 @@ +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[5] +Ig.file <- args[4] +outputfile <- args[6] +MAP.out<-args[7] +Sizesout <-args[8] + +#write.table(args,file=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") + #ReadIn=read.table(inputfile,stringsAsFactors=F,header=T, sep="\t", row.names=1) ##cms - changed on 11/18/13 + Names=names(ReadIn)[-1] + } +if(WhetherSampleName=="n"){ + ReadIn=read.table(inputfile,stringsAsFactors=F,header=F, sep="\t") + #ReadIn=read.table(inputfile,stringsAsFactors=F,header=F, sep="\t", row.names=1) ##cms - changed on 11/18/13 + 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 +IgVIn=read.table(Ig.file,stringsAsFactors=F,header=F,sep="\t") +IgV=IgVIn[[1]] + +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) +#write.table(Conditions,file=outputfile,quote=F,col.names=T,row.names=T,sep = "\t") +EBOut=EBMultiTest(Data=GeneMat,NgVector=IgV,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 11/20/13 +#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 11/20/13 +write.table(Sizes,file=Sizesout,quote=F,col.names=F,row.names=F,sep = "\t") + |