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32
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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[4]
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14 outputfile <- args[5]
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15 MAP.out<-args[6]
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16 Sizesout <-args[7]
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17
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18 #write.table(PatternFile,outputfile,quote=F,col.names=T,row.names=T,sep = "\t")
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19
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20 #write.table(args,outputfile,quote=F,col.names=T,row.names=T,sep = "\t")
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21
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22 Conditions=strsplit(CondIn,split=",")[[1]]
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23
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24 if(WhetherSampleName=="y"){
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25 ReadIn=read.table(inputfile,stringsAsFactors=F,header=T, sep="\t")
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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 Names=paste0("S",1:length(Conditions))
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31 }
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32
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33 #PatternIn=read.table(PatternFile,stringsAsFactors=F,header=T,sep="\t")
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34 PatternIn=read.table(PatternFile,stringsAsFactors=F,header=T,sep="\t",row.names=1) ##cms - changed on 11/15/13
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35
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36 if(class(ReadIn[[1]])=="character"){
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37 GeneMat=do.call(cbind,ReadIn[-1])
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38 rownames(GeneMat)=ReadIn[[1]]
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39 colnames(GeneMat)=Names
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40 }
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41 if(class(ReadIn[[1]])=="numeric"){
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42 GeneMat=data.matrix(ReadIn)
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43 colnames(GeneMat)=Names
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44 }
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45
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46 Patterns=data.matrix(PatternIn)
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47
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48
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49 Sizes=MedianNorm(GeneMat)
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50 EBOut=EBMultiTest(Data=GeneMat,Conditions=as.factor(Conditions),
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51 AllParti=Patterns,sizeFactors=Sizes, maxround=5)
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52 PPout=GetMultiPP(EBOut)
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53 MultiPP=PPout$PP
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54 MultiMAP=PPout$MAP
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55 Data.norm=round(GetNormalizedMat(GeneMat, Sizes),2)
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56
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57 Mat=cbind(MultiMAP,Data.norm[names(MultiMAP),])
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58
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59 colnames(Mat)=
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60 c("MAP",Names)
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61 options(warn=-1)
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62
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63 #write.table(round(MultiPP,2),file=outputfile,quote=F,col.names=T,row.names=T,sep = "\t")
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64 write.table(round(MultiPP,2),file=outputfile,quote=F,col.names=NA,row.names=T,sep = "\t") ##cms - changed on 11/15/13
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65 #write.table(Mat,file=MAP.out ,quote=F,col.names=T,row.names=T,sep = "\t")
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66 write.table(Mat,file=MAP.out ,quote=F,col.names=NA,row.names=T,sep = "\t") ##cms - changed on 11/15/13
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67 write.table(Sizes,file=Sizesout,quote=F,col.names=F,row.names=F,sep = "\t")
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68
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