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Commit id: 736588e3d47fd58358f61ce2241bb2c85b4d9a0c

update to vignette to process previously unevaluated codechunks

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-09-19 10:14:04 -0400
Author date: 2014-09-19 10:14:04 -0400


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@94285 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 19/09/2014 14:22:04
Showing4 changed files

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@@ -2,8 +2,8 @@ Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
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-Version: 1.23.2
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-Date: Mon Aug 25 21:43:53 EDT 2014
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+Version: 1.23.3
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+Date: Fri Sep 19 10:10:31 EDT 2014
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 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
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         Ruczinski, Rafael A Irizarry
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 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
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@@ -681,7 +681,7 @@ setMethod(OligoSetList, "CNSet", function(object,...){
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 	constructOligoSetListFrom(object, ...)
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 })
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 setMethod(BafLrrSetList, "CNSet", function(object,...){
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-	constructBafLrrSetListFrom(object, ...)
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+  constructBafLrrSetListFrom(object, ...)
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 })
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... ...
@@ -689,41 +689,41 @@ setMethod(BafLrrSetList, "CNSet", function(object,...){
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 constructOligoSetListFrom <- function(object, ...){
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-	##row.index <- seq_len(nrow(object))
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-	##col.index <- seq_len(ncol(object))
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-	is.lds <- ifelse(is(calls(object), "ff_matrix") | is(calls(object), "ffdf"), TRUE, FALSE)
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-	if(is.lds) stopifnot(isPackageLoaded("ff"))
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-	b.r <- calculateRBaf(object, ...)
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-	b <- b.r[["baf"]]
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-	r <- b.r[["lrr"]]
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-	j <- match(colnames(r[[1]]), sampleNames(object))
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-	rns <- lapply(r, rownames)
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-	fDList <- foreach(featureid=rns) %do%{
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-		featureData(object)[match(featureid, featureNames(object)), ]
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-	}
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-	names(fDList) <- sapply(fDList, function(x) chromosome(x)[1])
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-	gtPlist <- gtlist <- vector("list", length(r))
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-	for(i in seq_along(r)){
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-		gtlist[[i]] <- initializeBigMatrix("call", nr=nrow(r[[i]]), nc=length(j), vmode="integer")
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-		gtPlist[[i]] <- initializeBigMatrix("callPr", nr=nrow(r[[i]]), nc=length(j), vmode="integer")
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-		featureid <- rownames(r[[i]])
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-		ix <- match(featureid, featureNames(object))
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-		rownames(gtPlist[[i]]) <- rownames(gtlist[[i]]) <- featureid
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-		colnames(gtPlist[[i]]) <- colnames(gtlist[[i]]) <- colnames(r[[i]])
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-		for(k in seq_along(j)){
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-			gtlist[[i]][, k] <- calls(object)[ix, j[k]]
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-			gtPlist[[i]][, k] <- snpCallProbability(object)[ix, j[k]]
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-		}
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-	}
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-	ad <- AssayDataList(baf=b, copyNumber=r, call=gtlist, callProbability=gtPlist)
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-	object <- new("oligoSetList",
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-		      assayDataList=ad,
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-		      featureDataList=fDList,
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-		      chromosome=names(fDList),
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-		      phenoData=phenoData(object)[j, ],
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-		      annotation=annotation(object),
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-		      genome=genomeBuild(object))
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-	return(object)
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+  ##row.index <- seq_len(nrow(object))
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+  ##col.index <- seq_len(ncol(object))
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+  is.lds <- ifelse(is(calls(object), "ff_matrix") | is(calls(object), "ffdf"), TRUE, FALSE)
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+  if(is.lds) stopifnot(isPackageLoaded("ff"))
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+  b.r <- calculateRBaf(object, ...)
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+  b <- b.r[["baf"]]
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+  r <- b.r[["lrr"]]
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+  j <- match(colnames(r[[1]]), sampleNames(object))
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+  rns <- lapply(r, rownames)
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+  fDList <- foreach(featureid=rns) %do%{
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+    featureData(object)[match(featureid, featureNames(object)), ]
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+  }
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+  names(fDList) <- sapply(fDList, function(x) chromosome(x)[1])
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+  gtPlist <- gtlist <- vector("list", length(r))
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+  for(i in seq_along(r)){
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+    gtlist[[i]] <- initializeBigMatrix("call", nr=nrow(r[[i]]), nc=length(j), vmode="integer")
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+    gtPlist[[i]] <- initializeBigMatrix("callPr", nr=nrow(r[[i]]), nc=length(j), vmode="integer")
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+    featureid <- rownames(r[[i]])
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+    ix <- match(featureid, featureNames(object))
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+    rownames(gtPlist[[i]]) <- rownames(gtlist[[i]]) <- featureid
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+    colnames(gtPlist[[i]]) <- colnames(gtlist[[i]]) <- colnames(r[[i]])
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+    for(k in seq_along(j)){
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+      gtlist[[i]][, k] <- calls(object)[ix, j[k]]
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+      gtPlist[[i]][, k] <- snpCallProbability(object)[ix, j[k]]
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+    }
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+  }
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+  ad <- AssayDataList(baf=b, copyNumber=r, call=gtlist, callProbability=gtPlist)
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+  object <- new("oligoSetList",
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+                assayDataList=ad,
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+                featureDataList=fDList,
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+                chromosome=names(fDList),
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+                phenoData=phenoData(object)[j, ],
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+                annotation=annotation(object),
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+                genome=genomeBuild(object))
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+  return(object)
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 }
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@@ -77,7 +77,8 @@ the path indicated by \verb+outdir+.
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 <<setup>>=
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 pathToCels <- "/thumper/ctsa/snpmicroarray/hapmap/raw/affy/1m"
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-outdir <- paste("/local_data/r00/crlmm/", getRversion(), "/affy_vignette", sep="")
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+v <- paste0("crlmm_v", gsub("\\.", "_", packageDescription("crlmm")$Version))
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+outdir <- file.path("/thumper/ctsa/snpmicroarray/rs/ProcessedData", v)
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 dir.create(outdir, recursive=TRUE, showWarnings=FALSE)
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 @
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@@ -200,8 +200,7 @@ Estimation of log R ratios and B allele frequencies from an object of class \Rcl
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 crlmmCopynumber(cnSet, fit.linearModel=FALSE)
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 @
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-<<oligoSnpSet,eval=FALSE>>=
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-library(VanillaICE)
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+<<oligoSnpSet>>=
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 open(cnSet)
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 oligoSetList <- BafLrrSetList(cnSet)
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 close(cnSet)
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@@ -214,7 +213,7 @@ oligoSetList[[1]]
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 \noindent Log R ratios and B allele frequences can be retrieved by the
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 accessors \Rfunction{lrr} and \Rfunction{baf}, respectively.
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-<<testEqual,eval=FALSE>>=
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+<<testEqual>>=
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 lrrList <- lrr(oligoSetList)
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 class(lrrList)
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 dim(lrrList[[1]]) ## log R ratios for chromosome 1.