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remove callSet from genotype.Illumina args

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@53854 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 18/03/2011 01:57:35
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@@ -1251,20 +1251,17 @@ genotype.Illumina <- function(sampleSheet=NULL,
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 			      recallRegMin=1000,
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 			      gender=NULL,
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 			      returnParams=TRUE,
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-			      badSNP=0.7,
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-			      callSet) {
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+			      badSNP=0.7) {
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 	is.lds = ifelse(isPackageLoaded("ff"), TRUE, FALSE)
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 	stopifnot(is.lds)
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 	if(missing(cdfName)) stop("must specify cdfName")
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 	if(!isValidCdfName(cdfName)) stop("cdfName not valid.  see validCdfNames")
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         pkgname = getCrlmmAnnotationName(cdfName)
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-	if(missing(callSet) | !validObject(callSet)){
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-		callSet <- construct.Illumina(sampleSheet=sampleSheet, arrayNames=arrayNames,
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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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-	}
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 	## Basic checks
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 	##check that mixtureParams provided
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 	if(missing(mixtureParams))