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44
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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 outputfile <- args[3]
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13 Boxplots<-args[4]
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14 Sizesout <-args[5]
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15
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16 print(args)
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17
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18 if(WhetherSampleName=="y"){
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19 ReadIn=read.table(inputfile,stringsAsFactors=F,header=T, sep="\t")
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20 Names=names(ReadIn)[-1]
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21 }
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22 if(WhetherSampleName=="n"){
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23 ReadIn=read.table(inputfile,stringsAsFactors=F,header=F, sep="\t")
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24 Names=paste0("S",1:(length(ReadIn[1,])-1)) ##cms - added 11/11/13
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25 }
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26
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27 GeneMat=do.call(cbind,ReadIn[-1])
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28 rownames(GeneMat)=ReadIn[[1]]
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29 if(WhetherSampleName=="y")colnames(GeneMat)=Names
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30 if(WhetherSampleName=="n")colnames(GeneMat)=Names ##cms - added 11/11/13
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31
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32 Sizes=MedianNorm(GeneMat)
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33
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34 Data.norm=GetNormalizedMat(GeneMat, Sizes)
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35
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36 #write.table(round(Data.norm,2),file=outputfile,quote=F,col.names=T,row.names=T,sep = "\t")
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37 write.table(round(Data.norm,2),file=outputfile,quote=F,col.names=NA,row.names=T,sep = "\t") ##cms - fixed on 11/11/13
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38 pdf(Boxplots)
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39 boxplot(Data.norm,log="y",ylim=c(10^-1,10^6),xlab="Sample",ylab="Normalized Expression") ##cms - added axis labels on 11/11/13
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40 dev.off()
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41
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42 write.table(Sizes,file=Sizesout,quote=F,col.names=F,row.names=F,sep = "\t")
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43
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