git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58662 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 01/10/2011 04:50:12
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@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: crlmm |
| 2 | 2 |
Type: Package |
| 3 | 3 |
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: 1.11.38 |
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+Version: 1.11.39 |
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Date: 2010-12-10 |
| 6 | 6 |
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 |
| 7 | 7 |
Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU> |
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@@ -248,7 +248,7 @@ genotypeAffy <- function(cnSet, mixtureParams, SNRMin=5, recallMin=10, |
| 248 | 248 |
recallRegMin=1000, |
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gender=NULL, badSNP=0.7, returnParams=TRUE, |
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verbose=TRUE){
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- snp.index <- which(isSnp(cnSet)) |
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+ ##snp.index <- which(isSnp(cnSet)) |
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tmp <- crlmmGT2(A=calls(cnSet), |
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B=snpCallProbability(cnSet), |
| 254 | 254 |
SNR=cnSet$SNR, |
| ... | ... |
@@ -262,8 +262,8 @@ genotypeAffy <- function(cnSet, mixtureParams, SNRMin=5, recallMin=10, |
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gender=gender, |
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verbose=verbose, |
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returnParams=returnParams, |
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- badSNP=badSNP, |
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- snp.names=featureNames(cnSet)[snp.index]) |
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+ badSNP=badSNP) |
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+## snp.names=featureNames(cnSet)[snp.index]) |
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if(verbose) message("Genotyping finished. Updating container with genotype calls and confidence scores.")
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| 268 | 268 |
open(cnSet$gender) |
| 269 | 269 |
cnSet$gender[,] <- tmp[["gender"]] |