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commented replacement method for snpCallProbability.

Added testing.Rnw and testingFF.Rnw to Makefile

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48960 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:50:00
Showing4 changed files

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@@ -51,13 +51,15 @@ getFeatureData.Affy <- function(cdfName, copynumber=FALSE){
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 	return(new("AnnotatedDataFrame", data=data.frame(M)))
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 }
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-construct <- function(filenames, cdfName, copynumber=FALSE,
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+construct <- function(filenames,
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+		      cdfName,
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+		      copynumber=TRUE,
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 		      sns, verbose=TRUE, batch, fns){
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 	if(!missing(batch)){
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 		stopifnot(length(batch) == length(sns))
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 	}
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 	if(missing(sns) & missing(filenames)) stop("one of filenames or samplenames (sns) must be provided")
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-	if(verbose) message("Initializing container for assay data elements alleleA, alleleB, call, callProbability")
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+	if(verbose) message("Initializing container for copy number estimation")
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 	featureData <- getFeatureData.Affy(cdfName, copynumber=copynumber)
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 	if(!missing(fns)){
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 		index <- match(fns, featureNames(featureData))
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@@ -254,9 +256,8 @@ genotype <- function(filenames,
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 		A(callSet)[snp.index, ] <- snprmaRes[["A"]]
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 		B(callSet)[snp.index, ] <- snprmaRes[["B"]]
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 	}
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-##	stopifnot(identical(featureNames(callSet)[snp.index], snprmaRes$gns))
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-	pData(callSet)$SKW <- snprmaRes$SKW
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-	pData(callSet)$SNR <- snprmaRes$SNR
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+	pData(callSet)$SKW <- snprmaRes[["SKW"]]
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+	pData(callSet)$SNR <- snprmaRes[["SNR"]]
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 	mixtureParams <- snprmaRes$mixtureParams
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 	np.index <- which(!is.snp)
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 	if(verbose) message("Normalizing nonpolymorphic markers")
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@@ -432,7 +432,7 @@ setReplaceMethod("snpCall", c("CNSet", "ff_or_matrix"),
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                  function(object, ..., value){
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 			 assayDataElementReplace(object, "call", value)
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 		 })
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-setReplaceMethod("snpCallProbability", c("CNSet", "ff_or_matrix"),
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-                 function(object, ..., value){
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-			 assayDataElementReplace(object, "callProbability", value)
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-		 })
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+##setReplaceMethod("snpCallProbability", c("CNSet", "ff_or_matrix"),
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+##                 function(object, ..., value){
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+##			 assayDataElementReplace(object, "callProbability", value)
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+##		 })
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@@ -1,6 +1,16 @@
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 ## Need to submit from a fat node!
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 all:	illumina_copynumber copynumber 
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+testing: testing.Rnw
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+	echo "Stangle(\"testing.Rnw\")" | R --no-save --no-restore;	
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+	cat ~/bin/cluster.template | perl -pe "s/Rprog/testing.R/" > testing.R.sh
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+	qsub -m e -r y -cwd -l mem_free=12G,h_vmem=16G testing.R.sh
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+
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+testingFF: testingFF.Rnw
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+	echo "Stangle(\"testingFF.Rnw\")" | R --no-save --no-restore;	
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+	cat ~/bin/cluster.template | perl -pe "s/Rprog/testingFF.R/" > testingFF.R.sh
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+	qsub -m e -r y -cwd -l mem_free=12G,h_vmem=16G testingFF.R.sh
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+
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 copynumber:	copynumber.Rnw
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 	echo "Stangle(\"copynumber.Rnw\")" | R --no-save --no-restore;	
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 	cat ~/bin/cluster.template | perl -pe "s/Rprog/copynumber.R/" > copynumber.R.sh
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@@ -143,7 +143,7 @@ second time.
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 <<genotype>>=
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 tmpdir <- "~/tmp3"
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-stop()
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+##stop()
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 ##if(FALSE){
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 ##if(file.exists(tmpdir)) unlink(tmpdir, recursive=TRUE)
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 dir.create(tmpdir)