Browse code

Save callSet after construct.Illumina in the genotype.illumina function

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52838 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 15:58:32
Showing1 changed files

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@@ -1123,13 +1123,12 @@ genotype.Illumina = function(sampleSheet=NULL,
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         pkgname = getCrlmmAnnotationName(cdfName)
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 #        if(missing(outdir))
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 #          stop("Must specify a directory to store large data objects")
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-	callSet = construct.Illumina(sampleSheet=sampleSheet, arrayNames=arrayNames,
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-			                 ids=ids, path=path, arrayInfoColNames=arrayInfoColNames,
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-                             highDensity=highDensity, sep=sep, fileExt=fileExt,
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-			                 cdfName=cdfName, copynumber=copynumber, verbose=verbose, batch=batch, # fns=fns, 
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-                             saveDate=saveDate) #, outdir=outdir)
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+	callSet <- construct.Illumina(sampleSheet=sampleSheet, arrayNames=arrayNames,
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+				      ids=ids, path=path, arrayInfoColNames=arrayInfoColNames,
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+				      highDensity=highDensity, sep=sep, fileExt=fileExt,
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+				      cdfName=cdfName, copynumber=copynumber, verbose=verbose, batch=batch, # fns=fns, 
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+				      saveDate=saveDate) #, outdir=outdir)
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 	if(missing(sns)) sns = sampleNames(callSet)
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-    
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     if(is.lds) {
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 		open(A(callSet))
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 		open(B(callSet))
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@@ -1328,4 +1327,4 @@ processIDAT =  function(sel, sampleSheet=NULL,
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         rm(res)
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 		gc()
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         TRUE
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-      }
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\ No newline at end of file
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+      }