Mercurial > repos > ning > ebseq

comparison EBGeneTwoCondTest.R @ 34:360c058ed13a draft

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author ning
date Mon, 16 Jun 2014 16:22:44 -0400
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33:8a576d034d70 34:360c058ed13a
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 FDR <- args[4]
14 outputfile <- args[5]
15 Sort.out<-args[6]
16 Sort.out.FDR <-args[7]
17 Sizesout <-args[8]
18
19 Conditions=strsplit(CondIn,split=",")[[1]]
20
21 if(WhetherSampleName=="y"){
22 ReadIn=read.table(inputfile,stringsAsFactors=F,header=T,sep="\t")
23 Names=names(ReadIn)[-1]
24 }
25 if(WhetherSampleName=="n"){
26 ReadIn=read.table(inputfile,stringsAsFactors=F,header=F,sep="\t")
27 Names=paste0("S",1:length(Conditions))
28 }
29
30 if(class(ReadIn[[1]])=="character"){
31 GeneMat=do.call(cbind,ReadIn[-1])
32 rownames(GeneMat)=ReadIn[[1]]
33 colnames(GeneMat)=Names
34 }
35 if(class(ReadIn[[1]])=="numeric"){
36 GeneMat=data.matrix(ReadIn)
37 colnames(GeneMat)=Names
38 }
39
40
41 Sizes=MedianNorm(GeneMat)
42 EBOut=EBTest(Data=GeneMat,Conditions=as.factor(Conditions),sizeFactors=Sizes, maxround=5)
43 PP=GetPP(EBOut)
44 PP.sort=sort(PP,decreasing=T)
45 PP.sort.FDR=PP.sort[which(PP.sort>=1-as.numeric(FDR))]
46
47 Data.norm=GetNormalizedMat(GeneMat, Sizes)
48 FC=PostFC(EBOut)
49 realFC=FC[[2]]
50 postFC=FC[[1]]
51
52 Mat=cbind(PP, realFC[names(PP)], postFC[names(PP)],Data.norm[names(PP),])
53 Mat.sort=cbind(PP.sort, realFC[names(PP.sort)], postFC[names(PP.sort)],Data.norm[names(PP.sort),])
54
55
56 if(length(PP.sort.FDR)>1)Mat.sort.FDR=cbind(PP.sort.FDR, realFC[names(PP.sort.FDR)], postFC[names(PP.sort.FDR)],Data.norm[names(PP.sort.FDR),])
57
58 if(length(PP.sort.FDR)==1)Mat.sort.FDR=matrix(
59 c(PP.sort.FDR, realFC[names(PP.sort.FDR)], postFC[names(PP.sort.FDR)],Data.norm[names(PP.sort.FDR),])
60 ,nrow=1)
61
62 colnames(Mat)=colnames(Mat.sort)=
63 c("PPDE","RealFC","PosteriorFC",colnames(Data.norm))
64 if(length(PP.sort.FDR)>0)colnames(Mat.sort.FDR)=
65 c("PPDE","RealFC","PosteriorFC",colnames(Data.norm))
66
67 ##cms - col.names changed below to have a header for the row names. This way the output of RSEM can be joined with EBSeq output
68 #write.table(round(Mat,2),file=outputfile,quote=F,col.names=T,row.names=T,sep = "\t")
69 #write.table(round(Mat,2),file=outputfile,quote=F,col.names=NA,row.names=T,sep = "\t") ##cms - made correction on 11/11/13
70 write.table(round(Mat,2),file=outputfile,quote=F,col.names=c("gene_id\tPPDE","RealFC","PosteriorFC",colnames(Data.norm)),row.names=T,sep = "\t") ##cms - made correction on 11/11/13
71 #write.table(round(Mat.sort,2),file=Sort.out ,quote=F,col.names=T,row.names=T,sep = "\t")
72 #write.table(round(Mat.sort,2),file=Sort.out ,quote=F,col.names=NA,row.names=T,sep = "\t") ##cms - made correction on 11/11/13
73 write.table(round(Mat.sort,2),file=Sort.out ,quote=F,col.names=c("gene_id\tPPDE","RealFC","PosteriorFC",colnames(Data.norm)),row.names=T,sep = "\t") ##cms - made correction on 11/11/13
74 #if(length(PP.sort.FDR)>0)write.table(round(Mat.sort.FDR,2),file=Sort.out.FDR,quote=F,col.names=T,row.names=T,sep = "\t")
75 #if(length(PP.sort.FDR)>0)write.table(round(Mat.sort.FDR,2),file=Sort.out.FDR,quote=F,col.names=NA,row.names=T,sep = "\t") ##cms - made correction on 11/11/13
76 if(length(PP.sort.FDR)>0)write.table(round(Mat.sort.FDR,2),file=Sort.out.FDR,quote=F,col.names=c("gene_id\tPPDE","RealFC","PosteriorFC",colnames(Data.norm)),row.names=T,sep = "\t") ##cms - made correction on 12/17/13; this preserves the header if merged with RSEM output.
77 write.table(Sizes,file=Sizesout,quote=F,col.names=F,row.names=F,sep = "\t")
78