@@ -12,3 +12,4 @@ sample.CNSetLMff.rda

 extdata*

 copynumber-*

 copynumber.log

+*.log

@@ -117,6 +117,7 @@ genotype <- function(filenames,

 			     sns=sns,

 			     verbose=verbose,

 			     batch=batch)

+	##save(callSet, file=file.path(outdir, "callSet.rda"))

 	open(callSet)

 	mixtureParams <- matrix(NA, 4, length(filenames))

 	is.snp <- isSnp(callSet)

@@ -139,9 +140,9 @@ genotype <- function(filenames,

 	if(is.lds){

 		open(snprmaRes[["A"]])

 		open(snprmaRes[["B"]])

-		bb = ocProbesets()*ncol(A)*8

-		ffrowapply(A(callSet)[i1:i2, ] <- snprmaRes[["A"]][i1:i2, ], X=snprmaRes[["A"]], BATCHBYTES=bb)

-		ffrowapply(B(callSet)[i1:i2, ] <- snprmaRes[["B"]][i1:i2, ], X=snprmaRes[["B"]], BATCHBYTES=bb)

+		##bb <- getOption("ffbatchbytes")

+		ffrowapply(A(callSet)[i1:i2, ] <- snprmaRes[["A"]][i1:i2, ], X=snprmaRes[["A"]])##, BATCHBYTES=bb)

+		ffrowapply(B(callSet)[i1:i2, ] <- snprmaRes[["B"]][i1:i2, ], X=snprmaRes[["B"]])##, BATCHBYTES=bb)

 	} else{

 		A(callSet)[snp.index, ] <- snprmaRes[["A"]]

 		B(callSet)[snp.index, ] <- snprmaRes[["B"]]

@@ -196,8 +197,8 @@ genotype <- function(filenames,

 	if(is.lds){

 		open(tmp[["calls"]])

 		open(tmp[["confs"]])

-		ffrowapply(snpCall(callSet)[i1:i2, ] <- tmp[["calls"]][i1:i2, ], X=tmp[["calls"]], BATCHBYTES=bb)

-		ffrowapply(snpCallProbability(callSet)[i1:i2, ] <- tmp[["confs"]][i1:i2, ], X=tmp[["confs"]], BATCHBYTES=bb)

+		ffrowapply(snpCall(callSet)[i1:i2, ] <- tmp[["calls"]][i1:i2, ], X=tmp[["calls"]])#, BATCHBYTES=bb)

+		ffrowapply(snpCallProbability(callSet)[i1:i2, ] <- tmp[["confs"]][i1:i2, ], X=tmp[["confs"]])#, BATCHBYTES=bb)

 		close(tmp[["calls"]])

 		close(tmp[["confs"]])

 	} else {

@@ -1380,7 +1381,8 @@ constructIlluminaAssayData <- function(np, snp, object, storage.mode="environmen

 	}

 	np <- lapply(np, stripnames)

 	snp <- lapply(snp, stripnames)

-	if(is(snp[[1]], "ff")){

+	is.ff <- is(snp[[1]], "ff") | is(snp[[1]], "ffdf")

+	if(is.ff){

 		lapply(snp, open)

 		open(calls(object))

 		open(snpCallProbability(object))

@@ -1393,7 +1395,7 @@ constructIlluminaAssayData <- function(np, snp, object, storage.mode="environmen

 	A.np <- np[[1]]

 	B.np <- np[[2]]

 	nc <- ncol(object)

-	if(is(A.snp, "ff")){

+	if(is.ff){

 		NA.vec <- rep(NA, nrow(A.np))

 		AA <- initializeBigMatrix("A", nr, nc, vmode="integer")

 		BB <- initializeBigMatrix("B", nr, nc, vmode="integer")

@@ -7,7 +7,7 @@ setMethod("Ns", signature(object="AssayData"),

 		  batchnames <- sampleNames(object)

 		  if(!missing.j) batchnames <- batchnames[j]

 		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")

-		  is.ff <- is(assayDataElement(object, "N.AA"), "ff")

+		  is.ff <- is(assayDataElement(object, "N.AA"), "ff") | is(assayDataElement(object, "N.AA"), "ffdf")

 		  if(is.ff){

 			  open(assayDataElement(object, "N.AA"))

 			  open(assayDataElement(object, "N.AB"))

@@ -38,7 +38,7 @@ setMethod("corr", signature(object="AssayData"),

 		  batchnames <- sampleNames(object)

 		  if(!missing.j) batchnames <- batchnames[j]

 		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")

-		  is.ff <- is(assayDataElement(object, "corrAA"), "ff")

+		  is.ff <- is(assayDataElement(object, "corrAA"), "ff") | is(assayDataElement(object, "corrAA"), "ffdf")

 		  if(is.ff){

 			  open(assayDataElement(object, "corrAA"))

 			  open(assayDataElement(object, "corrAB"))

new file mode 100644

Binary files /dev/null and b/inst/doc/illumina_copynumber.pdf differ