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calculateRBaf adds dimnames to the emission probability array just prior to its return.

previously we assigned the dimnames of the object 'a', but this was NULL.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58764 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 04/10/2011 16:12:43
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: 1.11.51
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+Version: 1.11.52
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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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@@ -547,6 +547,7 @@ setMethod("calculateRBaf", signature(object="CNSet"),
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 	J <- which(batch(object) == batch.name)
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 	a <- A(object)[, J, drop=FALSE]
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 	b <- B(object)[, J, drop=FALSE] ## NA's for b where nonpolymorphic
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+	dns <- dimnames(a)
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 	dimnames(a) <- dimnames(b) <- NULL
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 	obs.theta <- atan2(b, a)*2/pi
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@@ -588,7 +589,7 @@ setMethod("calculateRBaf", signature(object="CNSet"),
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 	r.expected[index.np, ] <- matrix(meds, length(index.np), ncol(a.np))
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 	lrr <- log2(obs.r/r.expected)
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-	dimnames(bf) <- dimnames(lrr) <- dimnames(a)
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+	dimnames(bf) <- dimnames(lrr) <- dns
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 	res <- list(baf=bf,
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 		    lrr=lrr)
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 	return(res)