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0
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1 args<-commandArgs(TRUE)
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2
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3 chip=args[1]
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4 dataset=args[2]
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5 workdir=args[3]
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6 celPath=args[4]
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7 chipPath=args[4]
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8 tumor=args[5]
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9 settingType=args[6]
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10 outputgraph=type.convert(args[7])
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11 tag=args[8]
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12
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13 if (tag=="")
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14 {
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15 tag=NULL
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16 }
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17
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18 library(MPAgenomics)
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19 setwd(workdir)
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20 if (settingType=="standard")
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21 {
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22 signalPreProcess(dataSetName=dataset, chipType=chip, dataSetPath=celPath,chipFilesPath=chipPath, path=workdir,createArchitecture=TRUE, savePlot=outputgraph, tags=tag)
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23 } else {
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24 signalPreProcess(dataSetName=dataset, chipType=chip, dataSetPath=celPath,chipFilesPath=chipPath, normalTumorArray=tumor, path=workdir,createArchitecture=TRUE, savePlot=outputgraph, tags=tag)
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25 } |
