Browse code

Add illumina_copynumber.pdf to package.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49895 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 04/10/2010 02:21:53
Showing4 changed files

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@@ -12,3 +12,4 @@ sample.CNSetLMff.rda
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 extdata*
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 copynumber-*
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 copynumber.log
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+*.log
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@@ -117,6 +117,7 @@ genotype <- function(filenames,
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 			     sns=sns,
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 			     verbose=verbose,
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 			     batch=batch)
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+	##save(callSet, file=file.path(outdir, "callSet.rda"))
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 	open(callSet)
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 	mixtureParams <- matrix(NA, 4, length(filenames))
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 	is.snp <- isSnp(callSet)
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@@ -139,9 +140,9 @@ genotype <- function(filenames,
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 	if(is.lds){
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 		open(snprmaRes[["A"]])
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 		open(snprmaRes[["B"]])
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-		bb = ocProbesets()*ncol(A)*8
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-		ffrowapply(A(callSet)[i1:i2, ] <- snprmaRes[["A"]][i1:i2, ], X=snprmaRes[["A"]], BATCHBYTES=bb)
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-		ffrowapply(B(callSet)[i1:i2, ] <- snprmaRes[["B"]][i1:i2, ], X=snprmaRes[["B"]], BATCHBYTES=bb)
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+		##bb <- getOption("ffbatchbytes")
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+		ffrowapply(A(callSet)[i1:i2, ] <- snprmaRes[["A"]][i1:i2, ], X=snprmaRes[["A"]])##, BATCHBYTES=bb)
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+		ffrowapply(B(callSet)[i1:i2, ] <- snprmaRes[["B"]][i1:i2, ], X=snprmaRes[["B"]])##, BATCHBYTES=bb)
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 	} else{
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 		A(callSet)[snp.index, ] <- snprmaRes[["A"]]
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 		B(callSet)[snp.index, ] <- snprmaRes[["B"]]
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@@ -196,8 +197,8 @@ genotype <- function(filenames,
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 	if(is.lds){
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 		open(tmp[["calls"]])
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 		open(tmp[["confs"]])
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-		ffrowapply(snpCall(callSet)[i1:i2, ] <- tmp[["calls"]][i1:i2, ], X=tmp[["calls"]], BATCHBYTES=bb)
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-		ffrowapply(snpCallProbability(callSet)[i1:i2, ] <- tmp[["confs"]][i1:i2, ], X=tmp[["confs"]], BATCHBYTES=bb)
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+		ffrowapply(snpCall(callSet)[i1:i2, ] <- tmp[["calls"]][i1:i2, ], X=tmp[["calls"]])#, BATCHBYTES=bb)
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+		ffrowapply(snpCallProbability(callSet)[i1:i2, ] <- tmp[["confs"]][i1:i2, ], X=tmp[["confs"]])#, BATCHBYTES=bb)
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 		close(tmp[["calls"]])
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 		close(tmp[["confs"]])
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 	} else {
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@@ -1380,7 +1381,8 @@ constructIlluminaAssayData <- function(np, snp, object, storage.mode="environmen
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 	}
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 	np <- lapply(np, stripnames)
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 	snp <- lapply(snp, stripnames)
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-	if(is(snp[[1]], "ff")){
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+	is.ff <- is(snp[[1]], "ff") | is(snp[[1]], "ffdf")
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+	if(is.ff){
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 		lapply(snp, open)
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 		open(calls(object))
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 		open(snpCallProbability(object))
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@@ -1393,7 +1395,7 @@ constructIlluminaAssayData <- function(np, snp, object, storage.mode="environmen
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 	A.np <- np[[1]]
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 	B.np <- np[[2]]
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 	nc <- ncol(object)
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-	if(is(A.snp, "ff")){
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+	if(is.ff){
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 		NA.vec <- rep(NA, nrow(A.np))
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 		AA <- initializeBigMatrix("A", nr, nc, vmode="integer")
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 		BB <- initializeBigMatrix("B", nr, nc, vmode="integer")
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@@ -7,7 +7,7 @@ setMethod("Ns", signature(object="AssayData"),
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 		  batchnames <- sampleNames(object)
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 		  if(!missing.j) batchnames <- batchnames[j]
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 		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
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-		  is.ff <- is(assayDataElement(object, "N.AA"), "ff")
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+		  is.ff <- is(assayDataElement(object, "N.AA"), "ff") | is(assayDataElement(object, "N.AA"), "ffdf")
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 		  if(is.ff){
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 			  open(assayDataElement(object, "N.AA"))
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 			  open(assayDataElement(object, "N.AB"))
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@@ -38,7 +38,7 @@ setMethod("corr", signature(object="AssayData"),
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 		  batchnames <- sampleNames(object)
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 		  if(!missing.j) batchnames <- batchnames[j]
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 		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
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-		  is.ff <- is(assayDataElement(object, "corrAA"), "ff")
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+		  is.ff <- is(assayDataElement(object, "corrAA"), "ff") | is(assayDataElement(object, "corrAA"), "ffdf")
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 		  if(is.ff){
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 			  open(assayDataElement(object, "corrAA"))
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 			  open(assayDataElement(object, "corrAB"))
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new file mode 100644
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Binary files /dev/null and b/inst/doc/illumina_copynumber.pdf differ