Mercurial > repos > ning > ebseq
view ChoosePatterns.R @ 37:e11c511a2bb5 draft
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author | ning |
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date | Mon, 16 Jun 2014 16:23:31 -0400 |
parents | 689cba393d6b |
children |
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sink(file="/tmp/none") sink("/dev/null") options(warn=-1) options(echo=F) #invisible("EBSeq") #suppressMessages(library("EBSeq")) ##cms - changed on 11/11/13. Don't need EBSeq package. args <- commandArgs(trailingOnly = T) inputfile <- args[1] Idx <- args[2] outputfile <- args[3] print(args) ReadIn=read.table(inputfile,stringsAsFactors=F,header=T, sep="\t") IndexIn=strsplit(Idx,split=",")[[1]] Index=as.numeric(IndexIn) #Mat=data.matrix(ReadIn) Mat=data.matrix(ReadIn[,-1]) ##cms - changed on 11/11/13. Otherwise pattern IDs are replaced with NA. rownames(Mat)=ReadIn[,1] ##cms - also added on 11/11/13 to add pattern IDs back in. Out=Mat[Index,] #write.table(Out,file=outputfile,quote=F,col.names=T,row.names=T,sep = "\t") write.table(Out,file=outputfile,quote=F,col.names=NA,row.names=T,sep = "\t") ##cms - changed on 11/11/13