@@ -60,6 +60,7 @@ exportMethods(open, "[", show, lM, lines)

 export(crlmm, 

        crlmmCopynumber, 

        crlmmIllumina, 

+       crlmmIllumina2,

        genotype, 

        readIdatFiles, 

        readIdatFiles2,

@@ -69,6 +70,7 @@ export(crlmm,

        genotype2, genotypeLD,

        batch,

        crlmmCopynumber2, crlmmCopynumberLD)

+export(constructIlluminaCNSet)

@@ -3159,3 +3159,23 @@ constructIlluminaAssayData <- function(np, snp, object, storage.mode="environmen

 			   CA=emptyMatrix,

 			   CB=emptyMatrix)

 }

+constructIlluminaCNSet <- function(res,

+				   cnAB,

+				   crlmmResult){

+	fD <- constructIlluminaFeatureData(c(res$gns, cnAB$gns), cdfName="human370v1c")

+	new.order <- order(fD$chromosome, fD$position)

+	fD <- fD[new.order, ]

+	aD <- constructIlluminaAssayData(cnAB, res, crlmmResult, order.index=new.order)

+	protocolData(crlmmResult)$batch <- vector("integer", ncol(crlmmResult))

+	container <- new("CNSetLM", 

+			 assayData=aD,

+			 phenoData=phenoData(crlmmResult),

+			 protocolData=protocolData(crlmmResult),

+			 featureData=fD,

+			 annotation="human370v1c")

+	lM(container) <- initializeParamObject(list(featureNames(container), unique(protocolData(container)$batch)))

+	container

+}

+				   

+				   

+

@@ -46,6 +46,7 @@ options(continue=" ")

 @ 

 <<libraries>>=

+library(ff)

 library(crlmm)

 crlmm:::validCdfNames()

 if(length(grep("development", sessionInfo()[[1]]$status)) == 1){

@@ -92,7 +93,7 @@ redfiles = all(file.exists(paste(arrayNames, "_Red.idat", sep="")))

 <<samplesToProcess2, echo=FALSE>>=

 ## To speed up repeated calls to Sweave 

 RG <- checkExists("RG", .path=outdir,

-		  .FUN=readIdatFiles,

+		  .FUN=readIdatFiles2,

 		  sampleSheet=samplesheet,

 		  path=dirname(arrayNames[1]),

 		  arrayInfoColNames=list(barcode=NULL, position="SentrixPosition"), 

@@ -100,7 +101,7 @@ RG <- checkExists("RG", .path=outdir,

 annotation(RG) <- "human370v1c"

 crlmmResult <- checkExists("crlmmResult",

 			   .path=outdir,

-			   .FUN=crlmmIllumina,

+			   .FUN=crlmmIllumina2,

 			   RG=RG,

 			   sns=pData(RG)$ID, 

 			   returnParams=TRUE,

@@ -111,7 +112,7 @@ protocolData(crlmmResult)$ScanDate <- protocolData(RG)$ScanDate

 @ 

 <<samplesToProcess3, eval=FALSE>>=

-RG <- readIdatFiles(samplesheet, 

+RG <- readIdatFiles2(samplesheet[1:10, ], 

 		    path=dirname(arrayNames[1]), 

 		    arrayInfoColNames=list(barcode=NULL, position="SentrixPosition"), 

 		    saveDate=TRUE)

@@ -136,8 +137,9 @@ cnAB <- get("cnAB")

 @ 

 <<loadIntermediate, echo=FALSE>>=

-res <- checkExists("res", .path=outdir, .FUN=load, file=file.path(outdir, "snpFile.rda"))

-cnAB <- checkExists("cnAB", .path=outdir, .FUN=load, file=file.path(outdir, "cnFile.rda"))

+trace(checkExists, browser)

+res <- checkExists("snpFile", .path=outdir, .FUN=load, file=file.path(outdir, "snpFile.rda"))

+cnAB <- checkExists("cnFile", .path=outdir, .FUN=load, file=file.path(outdir, "cnFile.rda"))

 @ 

 After running the crlmm algorithm, we construct a container for

@@ -148,42 +150,19 @@ inst/scripts directory of this package and can be sourced as follows.

 Documentation for these helper functions will be available in the

 devel version of this package.

-<<constructContainer, eval=FALSE>>=

-path <- system.file("scripts", package="crlmm")

-source(file.path(path, "helperFunctions.R"))

-fD <- constructFeatureData(c(res$gns, cnAB$gns), cdfName="human370v1c")

-new.order <- order(fD$chromosome, fD$position)

-fD <- fD[new.order, ]

-aD <- constructAssayData(cnAB, res, crlmmResult, order.index=new.order)

-protocolData(crlmmResult)$batch <- vector("integer", ncol(crlmmResult))

-container <- new("CNSetLM", 

-		 assayData=aD,

-		 phenoData=phenoData(crlmmResult),

-		 protocolData=protocolData(crlmmResult),

-		 featureData=fD,

-		 annotation="human370v1c")

+<<constructContainer1, check=FALSE>>=

+container <- checkExists("container",

+			 .path=outdir,

+			 .FUN=constructIlluminaCNSet,

+			 res=res,

+			 cnAB=cnAB,

+			 crlmmResult=crlmmResult)

 @ 

-<<container2,echo=FALSE>>=

-if(!file.exists(file.path(outdir, "cnSet"))){

-	path <- system.file("scripts", package="crlmm")

-	source(file.path(path, "helperFunctions.R"))

-	fD <- constructFeatureData(c(res$gns, cnAB$gns), cdfName="human370v1c")

-	new.order <- order(fD$chromosome, fD$position)

-	fD <- fD[new.order, ]

-	aD <- constructAssayData(cnAB, res, crlmmResult, order.index=new.order)

-	protocolData(crlmmResult)$batch <- vector("integer", ncol(crlmmResult))

-	container <- new("CNSetLM", 

-			 assayData=aD,

-			 phenoData=phenoData(crlmmResult),

-			 protocolData=protocolData(crlmmResult),

-			 featureData=fD,

-			 annotation="human370v1c")

-}

+<<constructContainer2, eval=FALSE>>=

+container <- constructIlluminaCNSet(res=res, cnAB=cnAB, crlmmResult=crlmmResult)

 @ 

-

-

 As described in the \texttt{copynumber} vignette, two \R{} functions

 for copy number estimation are available: \Rfunction{crlmmCopynumber}

 and \Rfunction{crlmmCopynumber2}.  The latter requires that the assay

@@ -196,17 +175,14 @@ decided at the beginning of the analysis and then propogated to both

 the genotyping and copy number estimation steps.  Here, we use the

 \Rfunction{crlmmCopynumber} to estimate copy number.

-<<estimateCopynumber, echo=FALSE>>=

-if(!exists("cnSet")){

-	if(!file.exists(file.path(outdir, "cnSet.rda"))){

-		cnSet <- crlmmCopynumber(container, verbose=FALSE)

-		save(cnSet, file=file.path(outdir, "cnSet.rda"))

-	} else load(file.path(outdir, "cnSet.rda"))

-}

+<<estimateCopynumber1, echo=FALSE>>=

+cnSet <- checkExists("cnSet", .path=outdir,

+		     .FUN=crlmmCopynumberLD,

+		     object=container)

 @ 

 <<estimateCopynumber, eval=FALSE>>=

-cnSet <- crlmmCopynumber(container, verbose=TRUE)

+cnSet <- crlmmCopynumberLD(container)

 @ 

 %In the following code, we define helper functions to construct a