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Merge branch 'collab'

* collab:
update cnSet objects in data/
bump version
update version dependencies
coerce copy number and bafs to integer matrix in setAs(CNSet, oligoSnpSet)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@63707 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 10/03/2012 00:05:37
Showing5 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: 1.13.9
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+Version: 1.13.10
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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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@@ -9,8 +9,8 @@ Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays,
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 License: Artistic-2.0
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 Depends: R (>= 2.13.0),
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          methods,
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-         Biobase (>= 2.11.9),
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-         oligoClasses (>= 1.15.41)
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+         Biobase (>= 2.15.0),
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+         oligoClasses (>= 1.17.29)
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 Imports: affyio (>= 1.19.2),
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          ellipse,
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          genefilter (>= 1.33.0),
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@@ -42,17 +42,16 @@ cnSet2oligoSnpSet <- function(object){
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 ##	tcn[tcn > 8] <- 8
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 ##	log.tcn <- log2(tcn)
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 	tmp <- new("oligoSnpSet",
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-		   ##copyNumber=log.tcn,
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-		   copyNumber=b.r[[2]],
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-		   ##baf=b.r[[1]],
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+		   copyNumber=integerMatrix(b.r[[2]], scale=100),
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 		   call=calls(object),
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 		   callProbability=snpCallProbability(object),
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 		   annotation=annotation(object),
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 		   featureData=featureData(object),
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 		   phenoData=phenoData(object),
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 		   experimentData=experimentData(object),
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-		   protocolData=protocolData(object))
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-	tmp <- assayDataElementReplace(tmp, "baf", b.r[[1]])
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+		   protocolData=protocolData(object),
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+		   is.integer=FALSE)
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+	tmp <- assayDataElementReplace(tmp, "baf", integerMatrix(b.r[[1]], scale=1000))
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 	return(tmp)
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 }
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@@ -6,7 +6,7 @@ THISPKG <- "crlmm"
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 ##}
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 .onAttach <- function(libname, pkgname) {
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-	packageStartupMessage("Welcome to crlmm version ", packageDescription(THISPKG, field="Version"))
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+	packageStartupMessage("Welcome to crlmm version ", packageDescription(THISPKG, fields="Version"))
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 }
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 .onUnload <- function( libpath ){
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Binary files a/data/cnSetExample.rda and b/data/cnSetExample.rda differ
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Binary files a/data/cnSetExample2.rda and b/data/cnSetExample2.rda differ