Browse code

change cnSet$SNR and cnSet$SKW to numeric (previously ff)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@53657 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 12/03/2011 19:56:02
Showing8 changed files

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@@ -5,8 +5,6 @@ ffobjs*
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 auto*
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 ModelForPolymorphicX.pdf
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 .Rhistory
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-*.o
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-*.so
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 *.tex
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 illumina_copynumber-*
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 Makefile2
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@@ -1,7 +1,7 @@
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 Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
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-Version: 1.9.18
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+bVersion: 1.9.19
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 Date: 2010-12-10
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 Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry
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 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
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@@ -1160,9 +1160,10 @@ genotype.Illumina <- function(sampleSheet=NULL,
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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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+		sampleNames(callSet) <- basename(sampleNames(callSet))
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 		save(callSet, file=file.path(ldPath(), "callSet.rda"))
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 	} else message("Using callSet loaded from GlobalEnv")
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-	if(missing(sns)) sns = sampleNames(callSet)
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+	if(missing(sns)) sns = basename(sampleNames(callSet))
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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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@@ -1227,10 +1228,8 @@ genotype.Illumina <- function(sampleSheet=NULL,
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 		open(B(callSet))
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 		tmpA = initializeBigMatrix(name="tmpA", length(snp.index), narrays)
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 		tmpB = initializeBigMatrix(name="tmpB", length(snp.index), narrays)
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-		##          bb = getOption("ffbatchbytes")
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-		##          bb = ocProbesets()*length(sns)*8
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-		ffcolapply(tmpA[,i1:i2] <- A(callSet)[snp.index,i1:i2], X=A(callSet)) #, BATCHBYTES=bb) # X=A(callSet)[snp.index,]
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-		ffcolapply(tmpB[,i1:i2] <- B(callSet)[snp.index,i1:i2], X=B(callSet)) #, BATCHBYTES=bb) # X=B(callSet)[snp.index,]
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+		ffcolapply(tmpA[,i1:i2] <- A(callSet)[snp.index,i1:i2], X=A(callSet))
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+		ffcolapply(tmpB[,i1:i2] <- B(callSet)[snp.index,i1:i2], X=B(callSet))
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 		close(A(callSet))
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 		close(B(callSet))
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 		close(tmpA)
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@@ -1254,6 +1253,9 @@ genotype.Illumina <- function(sampleSheet=NULL,
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 ##		    verbose,
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 ##		    returnParams,
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 ##		    badSNP))
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+	save(tmpA, file=file.path(ldPath(), "tmpA.rda"))
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+	save(tmpB, file=file.path(ldPath(), "tmpB.rda"))
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+	save(mixtureParams, file=file.path(ldPath(), "mixtureParams.rda"))
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 	tmp <- crlmmGTfxn(FUN,
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 			  A=tmpA,
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 			  B=tmpB,
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