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No longer source helperFunctions.R. Use crlmm:::constructAssayData and crlmm:::constructFeatureData instead

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/crlmm@49108 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 15:45:30
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@@ -157,12 +157,12 @@ Documentation for these helper functions will be available in the
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 devel version of this package.
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 <<constructContainer, eval=FALSE>>=
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-path <- system.file("scripts", package="crlmm")
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-source(file.path(path, "helperFunctions.R"))
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-fD <- constructFeatureData(c(res$gns, cnAB$gns), cdfName="human370v1c")
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+##path <- system.file("scripts", package="crlmm")
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+##source(file.path(path, "helperFunctions.R"))
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+fD <- crlmm:::constructFeatureData(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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-aD <- constructAssayData(cnAB, res, crlmmResult, order.index=new.order)
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+aD <- crlmm:::constructAssayData(cnAB, res, crlmmResult, order.index=new.order)
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 protocolData(crlmmResult)$batch <- vector("integer", ncol(crlmmResult))
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 container <- new("CNSetLM",
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 		 assayData=aD,
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@@ -174,12 +174,12 @@ container <- new("CNSetLM",
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 <<container2,echo=FALSE>>=
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 if(!file.exists(file.path(outdir, "cnSet"))){
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-	path <- system.file("scripts", package="crlmm")
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-	source(file.path(path, "helperFunctions.R"))
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-	fD <- constructFeatureData(c(res$gns, cnAB$gns), cdfName="human370v1c")
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+	##path <- system.file("scripts", package="crlmm")
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+	##source(file.path(path, "helperFunctions.R"))
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+	fD <- crlmm:::constructFeatureData(c(res$gns, cnAB$gns), cdfName="human370v1c")
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 	new.order <- order(fD$chromosome, fD$position)
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 	fD <- fD[new.order, ]
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-	aD <- constructAssayData(cnAB, res, crlmmResult, order.index=new.order)
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+	aD <- crlmm:::constructAssayData(cnAB, res, crlmmResult, order.index=new.order)
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 	protocolData(crlmmResult)$batch <- vector("integer", ncol(crlmmResult))
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 	container <- new("CNSetLM",
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 			 assayData=aD,