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Issue8: genotypeInf.

Change call in genotypeInf to crlmmGT2 using the updated API for this function (remove snp.names from args)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58760 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 04/10/2011 16:11:49
Showing2 changed files

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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: 1.11.47
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+Version: 1.11.48
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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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@@ -1245,8 +1245,9 @@ genotypeInf <- function(cnSet, mixtureParams, probs=rep(1/3,3),
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 			  gender=gender,
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 			  verbose=verbose,
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 			  returnParams=returnParams,
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-			  badSNP=badSNP,
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-			  snp.names=featureNames(cnSet)[snp.index])
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+			  badSNP=badSNP)#,
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+	##RS:  I changed the API for crlmmGT2 to be consistent with crlmmGT
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+	## snp.names=featureNames(cnSet)[snp.index])
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 	if(verbose) message("Genotyping finished.  Updating container with genotype calls and confidence scores.")
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 	open(cnSet$gender)
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 	cnSet$gender[,] = tmp$gender