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
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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 |