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 @@ |
| 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: 1.13.4 |
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+Version: 1.13.5 |
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| 5 | 5 |
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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@@ -554,7 +554,8 @@ setMethod("calculateRBaf", signature(object="CNSet"),
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| 554 | 554 |
a <- A(object)[, J, drop=FALSE] |
| 555 | 555 |
b <- B(object)[, J, drop=FALSE] ## NA's for b where nonpolymorphic |
| 556 | 556 |
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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| 558 | 559 |
dns <- dimnames(a) |
| 559 | 560 |
dimnames(a) <- dimnames(b) <- NULL |
| 560 | 561 |
obs.theta <- atan2(b, a)*2/pi |