@@ -2,8 +2,8 @@ Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for

         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

-Version: 1.23.2

-Date: Mon Aug 25 21:43:53 EDT 2014

+Version: 1.23.3

+Date: Fri Sep 19 10:10:31 EDT 2014

 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo

         Ruczinski, Rafael A Irizarry

 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,

@@ -681,7 +681,7 @@ setMethod(OligoSetList, "CNSet", function(object,...){

 	constructOligoSetListFrom(object, ...)

 })

 setMethod(BafLrrSetList, "CNSet", function(object,...){

-	constructBafLrrSetListFrom(object, ...)

+  constructBafLrrSetListFrom(object, ...)

 })

@@ -689,41 +689,41 @@ setMethod(BafLrrSetList, "CNSet", function(object,...){

 constructOligoSetListFrom <- function(object, ...){

-	##row.index <- seq_len(nrow(object))

-	##col.index <- seq_len(ncol(object))

-	is.lds <- ifelse(is(calls(object), "ff_matrix") | is(calls(object), "ffdf"), TRUE, FALSE)

-	if(is.lds) stopifnot(isPackageLoaded("ff"))

-	b.r <- calculateRBaf(object, ...)

-	b <- b.r[["baf"]]

-	r <- b.r[["lrr"]]

-	j <- match(colnames(r[[1]]), sampleNames(object))

-	rns <- lapply(r, rownames)

-	fDList <- foreach(featureid=rns) %do%{

-		featureData(object)[match(featureid, featureNames(object)), ]

-	}

-	names(fDList) <- sapply(fDList, function(x) chromosome(x)[1])

-	gtPlist <- gtlist <- vector("list", length(r))

-	for(i in seq_along(r)){

-		gtlist[[i]] <- initializeBigMatrix("call", nr=nrow(r[[i]]), nc=length(j), vmode="integer")

-		gtPlist[[i]] <- initializeBigMatrix("callPr", nr=nrow(r[[i]]), nc=length(j), vmode="integer")

-		featureid <- rownames(r[[i]])

-		ix <- match(featureid, featureNames(object))

-		rownames(gtPlist[[i]]) <- rownames(gtlist[[i]]) <- featureid

-		colnames(gtPlist[[i]]) <- colnames(gtlist[[i]]) <- colnames(r[[i]])

-		for(k in seq_along(j)){

-			gtlist[[i]][, k] <- calls(object)[ix, j[k]]

-			gtPlist[[i]][, k] <- snpCallProbability(object)[ix, j[k]]

-		}

-	}

-	ad <- AssayDataList(baf=b, copyNumber=r, call=gtlist, callProbability=gtPlist)

-	object <- new("oligoSetList",

-		      assayDataList=ad,

-		      featureDataList=fDList,

-		      chromosome=names(fDList),

-		      phenoData=phenoData(object)[j, ],

-		      annotation=annotation(object),

-		      genome=genomeBuild(object))

-	return(object)

+  ##row.index <- seq_len(nrow(object))

+  ##col.index <- seq_len(ncol(object))

+  is.lds <- ifelse(is(calls(object), "ff_matrix") | is(calls(object), "ffdf"), TRUE, FALSE)

+  if(is.lds) stopifnot(isPackageLoaded("ff"))

+  b.r <- calculateRBaf(object, ...)

+  b <- b.r[["baf"]]

+  r <- b.r[["lrr"]]

+  j <- match(colnames(r[[1]]), sampleNames(object))

+  rns <- lapply(r, rownames)

+  fDList <- foreach(featureid=rns) %do%{

+    featureData(object)[match(featureid, featureNames(object)), ]

+  }

+  names(fDList) <- sapply(fDList, function(x) chromosome(x)[1])

+  gtPlist <- gtlist <- vector("list", length(r))

+  for(i in seq_along(r)){

+    gtlist[[i]] <- initializeBigMatrix("call", nr=nrow(r[[i]]), nc=length(j), vmode="integer")

+    gtPlist[[i]] <- initializeBigMatrix("callPr", nr=nrow(r[[i]]), nc=length(j), vmode="integer")

+    featureid <- rownames(r[[i]])

+    ix <- match(featureid, featureNames(object))

+    rownames(gtPlist[[i]]) <- rownames(gtlist[[i]]) <- featureid

+    colnames(gtPlist[[i]]) <- colnames(gtlist[[i]]) <- colnames(r[[i]])

+    for(k in seq_along(j)){

+      gtlist[[i]][, k] <- calls(object)[ix, j[k]]

+      gtPlist[[i]][, k] <- snpCallProbability(object)[ix, j[k]]

+    }

+  }

+  ad <- AssayDataList(baf=b, copyNumber=r, call=gtlist, callProbability=gtPlist)

+  object <- new("oligoSetList",

+                assayDataList=ad,

+                featureDataList=fDList,

+                chromosome=names(fDList),

+                phenoData=phenoData(object)[j, ],

+                annotation=annotation(object),

+                genome=genomeBuild(object))

+  return(object)

 }

@@ -77,7 +77,8 @@ the path indicated by \verb+outdir+.

 <<setup>>=

 pathToCels <- "/thumper/ctsa/snpmicroarray/hapmap/raw/affy/1m"

-outdir <- paste("/local_data/r00/crlmm/", getRversion(), "/affy_vignette", sep="")

+v <- paste0("crlmm_v", gsub("\\.", "_", packageDescription("crlmm")$Version))

+outdir <- file.path("/thumper/ctsa/snpmicroarray/rs/ProcessedData", v)

 dir.create(outdir, recursive=TRUE, showWarnings=FALSE)

 @

@@ -200,8 +200,7 @@ Estimation of log R ratios and B allele frequencies from an object of class \Rcl

 crlmmCopynumber(cnSet, fit.linearModel=FALSE)

 @

-<<oligoSnpSet,eval=FALSE>>=

-library(VanillaICE)

+<<oligoSnpSet>>=

 open(cnSet)

 oligoSetList <- BafLrrSetList(cnSet)

 close(cnSet)

@@ -214,7 +213,7 @@ oligoSetList[[1]]

 \noindent Log R ratios and B allele frequences can be retrieved by the

 accessors \Rfunction{lrr} and \Rfunction{baf}, respectively.

-<<testEqual,eval=FALSE>>=

+<<testEqual>>=

 lrrList <- lrr(oligoSetList)

 class(lrrList)

 dim(lrrList[[1]]) ## log R ratios for chromosome 1.