diff mpagenomics_normalize-7dc6ce39fb89/preprocess.R @ 0:84b13b0e2b85

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mpagenomics_normalize-7dc6ce39fb89/preprocess.R	Thu May 07 08:22:36 2015 -0400
@@ -0,0 +1,25 @@
+args<-commandArgs(TRUE)
+
+chip=args[1]
+dataset=args[2]
+workdir=args[3]
+celPath=args[4]
+chipPath=args[4]
+tumor=args[5]
+settingType=args[6]
+outputgraph=type.convert(args[7])
+tag=args[8]
+
+if (tag=="")
+{
+	tag=NULL
+}
+
+library(MPAgenomics)
+setwd(workdir)
+if (settingType=="standard")
+{
+	signalPreProcess(dataSetName=dataset, chipType=chip, dataSetPath=celPath,chipFilesPath=chipPath, path=workdir,createArchitecture=TRUE, savePlot=outputgraph, tags=tag)
+} else {
+	signalPreProcess(dataSetName=dataset, chipType=chip, dataSetPath=celPath,chipFilesPath=chipPath, normalTumorArray=tumor, path=workdir,createArchitecture=TRUE, savePlot=outputgraph, tags=tag)
+}
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