@@ -151,7 +151,7 @@ genotype <- function(filenames,

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

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

 		mixtureParams[, j] <- snprmaRes$mixtureParams

-		rm(snprmaRes); gc()

+		rm(snprmaRes); ##gc()

 		if(copynumber){

 			np.index <- which(isSnp(callSet) == 0)

 			cnrmaRes <- cnrma(filenames=filenames[j],

@@ -162,7 +162,7 @@ genotype <- function(filenames,

 					  verbose=verbose)

 			stopifnot(identical(featureNames(callSet)[np.index], rownames(cnrmaRes)))

 			A(callSet)[np.index, j] <- cnrmaRes

-			rm(cnrmaRes); gc()

+			rm(cnrmaRes); ##gc()

 		}

 		## as.matrix needed when ffdf is used

 		tmp <- crlmmGT(A=as.matrix(A(callSet)[snp.index, j]),

@@ -278,7 +278,7 @@ genotypeLD <- function(filenames,

 			   sns=sns,

 			   seed=seed,

 			   verbose=verbose)

-	rm(cnrmaRes); gc()

+	rm(cnrmaRes); ##gc()

 	## as.matrix needed when ffdf is used

 	tmp <- crlmmGT2(A=snprmaRes[["A"]],

 			B=snprmaRes[["B"]],

@@ -634,7 +634,7 @@ crlmmCopynumber <- function(object,

 					lM(object)[[k]][row.index, column] <- fData(tmp)[, k]

 				}

 			}			

-			rm(tmp); gc()

+			rm(tmp); ##gc()

 			ii <- ii+1

 		}

 	}

@@ -891,7 +891,7 @@ fit.lm1 <- function(idxBatch,

 			muB[index[[j]], -kk] <- mus[, 3:4]

 		}

 		rm(betahat, X, Y, mus, index, noAA, noAB, noBB, res)

-		gc()

+		##gc()

 		negA <- rowSums(muA < 0) > 0

 		negB <- rowSums(muB < 0) > 0

 		flags[, J] <- rowSums(Ns == 0) > 0

@@ -934,7 +934,7 @@ fit.lm1 <- function(idxBatch,

 ##		cA[, k] <- matrix((1/phiA[, J]*(A-nuA[, J])), nrow(A), ncol(A))

 ##		cB[, k] <- matrix((1/phiB[, J]*(B-nuB[, J])), nrow(B), ncol(B))

 		rm(G, A, B, NORM, wA, wB, YA,YB, res, negA, negB, Np, Ns)

-		gc()

+		##gc()

 	}

 ##	cA[cA < 0.05] <- 0.05

 ##	cB[cB < 0.05] <- 0.05

@@ -1276,7 +1276,7 @@ fit.lm3 <- function(idxBatch,

 ##		cA[, k] <- (A-nuA[, J]-phiA2[, J]*cB[, k])/phiA[, J]

 		##some of the snps are called for the men, but not the women

 		rm(YA, YB, wA, wB, res, tmp, phistar, A, B, G, index)

-		gc()

+		##gc()

 	}

 ##	cA[cA < 0.05] <- 0.05

 ##	cB[cB < 0.05] <- 0.05

@@ -1479,7 +1479,7 @@ fit.lm4 <- function(idxBatch,

 ##		tmp[, gend==2] <- CT2

 ##		cA[, k] <- tmp

 		rm(tmp, CT1, CT2, A.F, normal.f, G, AA, BB, Y, X, Ns)

-		gc()

+		##gc()

 	}

 ##	cA[cA < 0.05] <- 0.05

 ##	cA[cA > 5] <-  5

@@ -2096,7 +2096,7 @@ locationAndScale <- function(object, cnOptions, tmp.objects){

 	index.AA <- index[[1]]

 	index.AB <- index[[2]]

 	index.BB <- index[[3]]

-	rm(index); gc()

+	rm(index); ##gc()

 	GT.A <- tmp.objects[["GT.A"]]

 	GT.B <- tmp.objects[["GT.B"]]

@@ -243,17 +243,36 @@ setMethod("CB",

 		  ##assayDataElement(object, "CB")

 		  browser()

 	  })

+

 setMethod("CA",

 	  signature=signature(object="CNSet", i="integerOrMissing", j="integerOrMissing"),

 	  function(object, i, j) {

 		  browser()

+		  if(missing(i) & missing(j)){

+			  if(inherits(A(object), "ff") | inherits(A(object), "ffdf")) stop("Must specify i and/or j for ff objects")

+		  }

+		  if(missing(i) & !missing(j)){

+			  ## calculate ca only for batches indexed by j

+			  batches <- unique(batch(object))[j]

+			  for(k in seq_along(batches)){

+				  bb <- batches[k]

+			  }

+		  }

+		  if(!missing(i) & missing(j)){

+			  ## calculate ca, cb for all batches

+			  batches <- unique(batch(object))

+		  }

+		  if(!missing(i) & !missing(j)){

+

+		  }

+		  return(ca)

 	  })

 setMethod("totalCopyNumber",

 	  signature=signature(object="CNSet", i="integerOrMissing", j="integerOrMissing"),

 	  function(object, i, j, ...){

 	if(missing(i) & missing(j)){

-		if(inherits(CA(object), "ff") | inherits(CA(object), "ffdf")) stop("Must specify i and/or j for ff objects")

+		if(inherits(A(object), "ff") | inherits(A(object), "ffdf")) stop("Must specify i and/or j for ff objects")

 	}

 	if(missing(i) & !missing(j)){

 		snp.index <- which(isSnp(object))	

@@ -145,7 +145,11 @@ computation had already been performed as part of the batch job.

 cnSet.assayData_matrix <- checkExists("cnSet.assayData_matrix",

 				      .path=outdir,

 				      .FUN=crlmmCopynumber,

-				      object=gtSet.assayData_matrix)

+				      object=gtSet.assayData_matrix,

+				      chromosome=22)

+Rprof(interval=0.1)

+obj <- crlmmCopynumber(gtSet.assayData_matrix, chromosome=22)

+Rprof(NULL)

 if(file.exists(file.path(outdir, "gtSet.assayData_matrix.rda")))

 	unlink(file.path(outdir, "gtSet.assayData_matrix.rda"))

 @ 

@@ -177,6 +181,7 @@ so that subsequent calls to \verb@Sweave@ can be run interactively.

 <<LDS_genotype>>=

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

+	library(ff)

 	gtSet.assayData_ff <- checkExists("gtSet.assayData_ff",

 					  .path=outdir,

 					  .FUN=genotypeLD,