Mercurial > repos > ning > ebseq

comparison EBIsoformMultiCondTest.R @ 36:7be90b1366d5 draft

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author ning
date Mon, 16 Jun 2014 16:23:21 -0400
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35:8b85a39cb625 36:7be90b1366d5
1 sink(file="/tmp/none")
2 sink("/dev/null")
3 options(warn=-1)
4 options(echo=F)
5
6 invisible("EBSeq")
7 suppressMessages(library("EBSeq"))
8
9 args <- commandArgs(trailingOnly = T)
10 inputfile <- args[1]
11 WhetherSampleName <- args[2]
12 CondIn <- args[3]
13 PatternFile <- args[5]
14 Ig.file <- args[4]
15 outputfile <- args[6]
16 MAP.out<-args[7]
17 Sizesout <-args[8]
18
19 #write.table(args,file=outputfile,quote=F,col.names=T,row.names=T,sep = "\t")
20
21
22 Conditions=strsplit(CondIn,split=",")[[1]]
23 if(WhetherSampleName=="y"){
24 ReadIn=read.table(inputfile,stringsAsFactors=F,header=T, sep="\t")
25 #ReadIn=read.table(inputfile,stringsAsFactors=F,header=T, sep="\t", row.names=1) ##cms - changed on 11/18/13
26 Names=names(ReadIn)[-1]
27 }
28 if(WhetherSampleName=="n"){
29 ReadIn=read.table(inputfile,stringsAsFactors=F,header=F, sep="\t")
30 #ReadIn=read.table(inputfile,stringsAsFactors=F,header=F, sep="\t", row.names=1) ##cms - changed on 11/18/13
31 Names=paste0("S",1:length(Conditions))
32 }
33
34 #PatternIn=read.table(PatternFile,stringsAsFactors=F,header=T,sep="\t")
35 PatternIn=read.table(PatternFile,stringsAsFactors=F,header=T,sep="\t",row.names=1) ##cms - changed on 11/15/13
36 IgVIn=read.table(Ig.file,stringsAsFactors=F,header=F,sep="\t")
37 IgV=IgVIn[[1]]
38
39 if(class(ReadIn[[1]])=="character"){
40 GeneMat=do.call(cbind,ReadIn[-1])
41 rownames(GeneMat)=ReadIn[[1]]
42 colnames(GeneMat)=Names
43 }
44 if(class(ReadIn[[1]])=="numeric"){
45 GeneMat=data.matrix(ReadIn)
46 colnames(GeneMat)=Names
47 }
48
49 Patterns=data.matrix(PatternIn)
50
51 Sizes=MedianNorm(GeneMat)
52 #write.table(Conditions,file=outputfile,quote=F,col.names=T,row.names=T,sep = "\t")
53 EBOut=EBMultiTest(Data=GeneMat,NgVector=IgV,Conditions=as.factor(Conditions),
54 AllParti=Patterns,sizeFactors=Sizes, maxround=5)
55 PPout=GetMultiPP(EBOut)
56 MultiPP=PPout$PP
57 MultiMAP=PPout$MAP
58 Data.norm=round(GetNormalizedMat(GeneMat, Sizes),2)
59
60 Mat=cbind(MultiMAP,Data.norm[names(MultiMAP),])
61
62 colnames(Mat)=
63 c("MAP",Names)
64 options(warn=-1)
65
66 #write.table(round(MultiPP,2),file=outputfile,quote=F,col.names=T,row.names=T,sep = "\t")
67 write.table(round(MultiPP,2),file=outputfile,quote=F,col.names=NA,row.names=T,sep = "\t") ##cms - changed on 11/20/13
68 #write.table(Mat,file=MAP.out ,quote=F,col.names=T,row.names=T,sep = "\t")
69 write.table(Mat,file=MAP.out ,quote=F,col.names=NA,row.names=T,sep = "\t") ##cms - changed on 11/20/13
70 write.table(Sizes,file=Sizesout,quote=F,col.names=F,row.names=F,sep = "\t")
71