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Intermediate files are loaded within the constructIlluminaCNSet function.

- Removed the loading of intermediate files from the vignette.
- Modified function constructIlluminaCNSet accordingly.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48625 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 02/08/2010 08:52:18
Showing2 changed files

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@@ -3159,9 +3159,13 @@ constructIlluminaAssayData <- function(np, snp, object, storage.mode="environmen
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 			   CA=emptyMatrix,
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 			   CB=emptyMatrix)
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 }
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-constructIlluminaCNSet <- function(res,
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-				   cnAB,
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-				   crlmmResult){
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+constructIlluminaCNSet <- function(crlmmResult,
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+				   snpFile,
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+				   cnFile){
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+	load(file.path(outdir, "snpFile.rda"))
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+	res <- get("res")
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+	load(file.path(outdir, "cnFile.rda"))
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+	cnAB <- get("cnAB")	
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 	fD <- constructIlluminaFeatureData(c(res$gns, cnAB$gns), cdfName="human370v1c")
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 	new.order <- order(fD$chromosome, fD$position)
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 	fD <- fD[new.order, ]
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@@ -117,7 +117,7 @@ RG <- readIdatFiles2(samplesheet[1:10, ],
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 		    arrayInfoColNames=list(barcode=NULL, position="SentrixPosition"), 
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 		    saveDate=TRUE)
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 annotation(RG) <- "human370v1c"
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-crlmmResult <- crlmmIllumina(RG=RG, 
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+crlmmResult <- crlmmIllumina2(RG=RG, 
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 			     cdfName="human370v1c", 
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 			     sns=pData(RG)$ID, 
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 			     returnParams=TRUE,
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@@ -127,20 +127,20 @@ crlmmResult <- crlmmIllumina(RG=RG,
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 protocolData(crlmmResult)$ScanDate <- protocolData(RG)$ScanDate
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 @ 
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-\noindent Finally, we load a few of the intermediate files that were
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-created during the preprocessing and genotyping.
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-<<loadIntermediate, eval=FALSE>>=
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-load(file.path(outdir, "snpFile.rda"))
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-res <- get("res")
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-load(file.path(outdir, "cnFile.rda"))
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-cnAB <- get("cnAB")
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-@ 
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-
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-<<loadIntermediate, echo=FALSE>>=
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-trace(checkExists, browser)
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-res <- checkExists("snpFile", .path=outdir, .FUN=load, file=file.path(outdir, "snpFile.rda"))
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-cnAB <- checkExists("cnFile", .path=outdir, .FUN=load, file=file.path(outdir, "cnFile.rda"))
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-@ 
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+%\noindent Finally, we load a few of the intermediate files that were
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+%created during the preprocessing and genotyping.
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+%<<loadIntermediate, eval=FALSE>>=
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+%load(file.path(outdir, "snpFile.rda"))
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+%res <- get("res")
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+%load(file.path(outdir, "cnFile.rda"))
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+%cnAB <- get("cnAB")
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+%@ 
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+%
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+%<<loadIntermediate, echo=FALSE>>=
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+%trace(checkExists, browser)
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+%res <- checkExists("snpFile", .path=outdir, .FUN=load, file=file.path(outdir, "snpFile.rda"))
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+%cnAB <- checkExists("cnFile", .path=outdir, .FUN=load, file=file.path(outdir, "cnFile.rda"))
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+%@ 
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 After running the crlmm algorithm, we construct a container for
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 storing the quantile normalized intensities, genotype calls, and
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@@ -154,9 +154,9 @@ devel version of this package.
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 container <- checkExists("container",
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 			 .path=outdir,
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 			 .FUN=constructIlluminaCNSet,
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-			 res=res,
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-			 cnAB=cnAB,
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-			 crlmmResult=crlmmResult)
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+			 crlmmResult=crlmmResult,
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+			 snpFile=snpFile,
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+			 cnFile=cnFile)
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 @ 
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 <<constructContainer2, eval=FALSE>>=