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Merge branch 'collab_release' into local_2_11

* collab_release:
remove trace() from vign.
only close callsGt when not missing
Fix the following bug in crlmmGT2 (only occurs when called from crlmm2):

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/crlmm@70636 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 18/10/2012 02:04:10
Showing3 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: 1.16.0
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+Version: 1.16.1
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 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, 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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 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
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@@ -208,7 +208,7 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,
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 	callsGt.present <- !missing(callsGt)
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 	callsPr.present <- !missing(callsPr)
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 	overwriteAB <- !callsGt.present & !callsPr.present
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-	if(overwriteAB){
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+	if(!overwriteAB){
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 		open(callsGt)
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 		open(callsPr)
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 	}
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@@ -246,7 +246,7 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,
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 	close(A)
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 	close(B)
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 	close(mixtureParams)
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-	if(overwriteAB){
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+	if(!overwriteAB){
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 		close(callsGt)
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 		close(callsPr)
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 	}
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@@ -22,7 +22,7 @@
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 options(width=60)
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 options(continue=" ")
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 options(prompt="R> ")
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-@ 
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+@
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 \section{Quick intro to \Rpackage{crlmm}}
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@@ -55,7 +55,7 @@ library(hapmapsnp6)
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 path <- system.file("celFiles", package="hapmapsnp6")
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 celFiles <- list.celfiles(path, full.names=TRUE)
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 system.time(crlmmResult <- crlmm(celFiles, verbose=FALSE))
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-@ 
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+@
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 The \Robject{crlmmResult} is a \Rclass{SnpSet} (see Biobase) object.
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 \begin{itemize}
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@@ -72,7 +72,7 @@ The \Robject{crlmmResult} is a \Rclass{SnpSet} (see Biobase) object.
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 calls(crlmmResult)[1:10,]
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 confs(crlmmResult)[1:10,]
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 crlmmResult[["SNR"]]
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-@ 
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+@
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 \section{Details}
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@@ -80,7 +80,7 @@ This document was written using:
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 <<>>=
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 sessionInfo()
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-@ 
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+@
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 \end{document}