Browse code

Make API for crlmmGT2 the same as crlmmGT. Define snpNames method for 'character'.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58661 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:50:07
Showing4 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: 1.11.37
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+Version: 1.11.38
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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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@@ -29,7 +29,7 @@ importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
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 		  "A<-", "B<-", open, close, flags,
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 		  openff, closeff,
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 		  batchStatistics, "batchStatistics<-", updateObject,
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-		  order, checkOrder)
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+		  order, checkOrder, snpNames)
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 importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,
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            copyNumber, initializeBigMatrix, initializeBigVector, isPackageLoaded)
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@@ -9,6 +9,18 @@ getProtocolData.Affy <- function(filenames){
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 			                           row.names=colnames(scanDates)))
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 	return(protocoldata)
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 }
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+
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+setMethod("snpNames", signature(object="character"),
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+	  function(object){
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+		  nm <- grep("Crlmm", object)
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+		  if(length(nm)==0){
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+			  pkgname <- paste(object, "Crlmm", sep="")
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+		  } else pkgname <- object
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+		  loader("preprocStuff.rda", .crlmmPkgEnv, object)
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+		  gns <- getVarInEnv("gns")
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+		  return(gns)
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+	  })
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+
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 getFeatureData <- function(cdfName, copynumber=FALSE){
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 	pkgname <- getCrlmmAnnotationName(cdfName)
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 	if(!require(pkgname, character.only=TRUE)){
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@@ -2,7 +2,7 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,
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                      col.names=NULL, probs=c(1/3, 1/3, 1/3), DF=6,
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                      SNRMin=5, recallMin=10, recallRegMin=1000,
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                      gender=NULL, desctrucitve=FALSE, verbose=TRUE,
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-                     returnParams=FALSE, badSNP=.7, snp.names){
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+                     returnParams=FALSE, badSNP=.7){
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 	pkgname <- getCrlmmAnnotationName(cdfName)
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 	stopifnot(require(pkgname, character.only=TRUE, quietly=!verbose))
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 	open(SNR)
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@@ -18,11 +18,14 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,
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 		stopifnot(nrow(A) == length(gns))
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 		index <- seq(length=nrow(A))
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 	}
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-	if(!missing(snp.names)){
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-		stopifnot(!is.null(rownames(A)))
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-		##verify that A has only snps.  otherwise, calling function must pass rownames
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-		index <- match(snp.names, rownames(A))
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-	}
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+	snp.names <- snpNames(pkgname)
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+	stopifnot(!is.null(rownames(A)))
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+	index <- match(snp.names, rownames(A))
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+##	if(!missing(snp.names)){
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+##
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+##		##verify that A has only snps.  otherwise, calling function must pass rownames
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+##		index <- match(snp.names, rownames(A))
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+##	}
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 	snpBatches <- splitIndicesByLength(index, ocProbesets())
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 	NR <- length(unlist(snpBatches))
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 	if(verbose) message("Calling ", NR, " SNPs for recalibration... ")