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Compute atan2(0, A)*2/pi for nonpolymorphic markers

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@62105 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 17/01/2012 19:11:45
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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: 1.13.4
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+Version: 1.13.5
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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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@@ -554,7 +554,8 @@ setMethod("calculateRBaf", signature(object="CNSet"),
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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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 		  is.np <- !isSnp(object)
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-		  b[is.np, ] <- a[is.np, ]
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+		  ##b[is.np, ] <- a[is.np, ]
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+		  b[is.np, ] <- 0L
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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