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1 args<-commandArgs(TRUE)
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2
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3 input=args[1]
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4 response=args[2]
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5 tmp_dir=args[3]
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6 nbFolds=as.numeric(args[4])
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7 loss=args[5]
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8 output=args[6]
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9
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10 library(MPAgenomics)
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11 workdir=file.path(tmp_dir, "mpagenomics")
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12 setwd(workdir)
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13
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14 CN=read.table(input,header=TRUE,check.names=FALSE)
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15 drops=c("chromosome","position","probeName")
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16 CNsignal=CN[,!(names(CN)%in% drops)]
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17 samples=names(CNsignal)
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18 CNsignalMatrix=t(data.matrix(CNsignal))
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19 resp=read.table(response,header=TRUE,sep=",")
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20 listOfFile=resp[[1]]
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21 responseValue=resp[[2]]
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22 index = match(listOfFile,rownames(CNsignalMatrix))
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23 responseValueOrder=responseValue[index]
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24
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25 result=variableSelection(CNsignalMatrix,responseValueOrder,nbFolds=nbFolds,loss=loss,plot=TRUE)
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26
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27 CNsignalResult=CN[result$markers.index,(names(CN)%in% drops)]
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28
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29 CNsignalResult["coefficient"]=result$coefficient
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30 CNsignalResult["index"]=result$markers.index
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31
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32 sink(output)
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33 print(format(CNsignalResult),row.names=FALSE)
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34 sink()
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35 #write.table(CNsignalResult,output,row.names = FALSE, quote=FALSE, sep = "\t")
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