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comparison EBIsoformMultiCondTest.R @ 9:c20070b11b55 draft

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author ning
date Fri, 15 Mar 2013 18:22:24 -0400
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8:03aa1c6fe091 9:c20070b11b55
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 Names=names(ReadIn)[-1]
26 }
27 if(WhetherSampleName=="n"){
28 ReadIn=read.table(inputfile,stringsAsFactors=F,header=F, sep="\t")
29 Names=paste0("S",1:length(Conditions))
30 }
31
32 PatternIn=read.table(PatternFile,stringsAsFactors=F,header=T,sep="\t")
33 IgVIn=read.table(Ig.file,stringsAsFactors=F,header=F,sep="\t")
34 IgV=IgVIn[[1]]
35
36 if(class(ReadIn[[1]])=="character"){
37 GeneMat=do.call(cbind,ReadIn[-1])
38 rownames(GeneMat)=ReadIn[[1]]
39 colnames(GeneMat)=Names
40 }
41 if(class(ReadIn[[1]])=="numeric"){
42 GeneMat=data.matrix(ReadIn)
43 colnames(GeneMat)=Names
44 }
45
46 Patterns=data.matrix(PatternIn)
47
48 Sizes=MedianNorm(GeneMat)
49 #write.table(Conditions,file=outputfile,quote=F,col.names=T,row.names=T,sep = "\t")
50 EBOut=EBMultiTest(Data=GeneMat,NgVector=IgV,Conditions=as.factor(Conditions),
51 AllParti=Patterns,sizeFactors=Sizes, maxround=5)
52 PPout=GetMultiPP(EBOut)
53 MultiPP=PPout$PP
54 MultiMAP=PPout$MAP
55 Data.norm=round(GetNormalizedMat(GeneMat, Sizes),2)
56
57 Mat=cbind(MultiMAP,Data.norm[names(MultiMAP),])
58
59 colnames(Mat)=
60 c("MAP",Names)
61 options(warn=-1)
62
63 write.table(round(MultiPP,2),file=outputfile,quote=F,col.names=T,row.names=T,sep = "\t")
64 write.table(Mat,file=MAP.out ,quote=F,col.names=T,row.names=T,sep = "\t")
65 write.table(Sizes,file=Sizesout,quote=F,col.names=F,row.names=F,sep = "\t")
66