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