@@ -2633,7 +2633,7 @@ thresholdModelParams <- function(object, cnOptions){

 	return(object)

 }

-computeCopynumber.CNSet <- function(object, cnOptions){

+cnCNSet <- function(object, cnOptions){

 	PLATE <- unique(batch(object))

 	verbose <- cnOptions$verbose

 	tmp.objects <- instantiateObjects(object, cnOptions)

@@ -2695,9 +2695,9 @@ computeCopynumber.CNSet <- function(object, cnOptions){

 	object <- pr(object, "corrA.BB", PLATE, getParam(object, "corrA.BB", PLATE))

 	object <- pr(object, "corrB.AA", PLATE, getParam(object, "corrB.AA", PLATE))

 	##object <- object[order(chromosome(object), position(object)), ]

-	if(cnOptions[["thresholdCopynumber"]]){

-		object <- thresholdCopynumber(object)

-	}

+##	if(cnOptions[["thresholdCopynumber"]]){

+##		object <- thresholdCopynumber(object)

+##	}

 	return(object)

 }

@@ -96,11 +96,11 @@ setMethod("computeCopynumber", "CNSet",

 	if(bias.adj & all(is.na(fData(object)$nuA_1))){

 		cnOptions[["bias.adj"]] <- FALSE

 	}

-	object <- computeCopynumber.CNSet(object, cnOptions)				

+	object <- cnCNSet(object, cnOptions)				

 	if(bias.adj & !cnOptions[["bias.adj"]]){

 		## Do a second iteration with bias adjustment

 		cnOptions[["bias.adj"]] <- TRUE

-		object <- computeCopynumber.CNSet(object, cnOptions)

+		object <- cnCNSet(object, cnOptions)

 	}

 	object

 })

@@ -212,9 +212,9 @@ getParam.SnpSuperSet <- function(object, name, batch){

 ##	saved.objects

 ##})

-setMethod("computeCopynumber", "SnpSuperSet",

-	  function(object, cnOptions){

-		  computeCopynumber.SnpSuperSet(object, cnOptions)

-	  })

+##setMethod("computeCopynumber", "SnpSuperSet",

+##	  function(object, cnOptions){

+##		  computeCopynumber.SnpSuperSet(object, cnOptions)

+##	  })

@@ -147,7 +147,7 @@ cnSet.assayData_matrix <- checkExists("cnSet.assayData_matrix",

 				      object=gtSet.assayData_matrix,

 				      chromosome=22)

 ##Rprof(interval=0.1)

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

+obj <- crlmmCopynumber(gtSet.assayData_matrix, chromosome=23)

 ##Rprof(NULL)

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

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

@@ -376,20 +376,23 @@ genotypeConf <- integerScoreToProbability(snpCallProbability(x)[snp.index[1:10],

 Allele-specific copy number at polymorphic loci:

 <<ca>>=

 ##ca <- CA(x[snp.index, ])/100

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

-ca <- CA(obj, i=snp.index)

+snp.index <- which(isSnp(x))

+ca <- CA(x, i=snp.index)

 ##or

-ca <- ACN(obj, "A", i=snp.index)

+ca <- ACN(x, "A", i=snp.index)

+cb <- CB(x, i=snp.index)

+ct <- ca+cb

 @ 

 Total copy number at nonpolymorphic loci:

 <<ca>>=

-cn.nonpolymorphic <- CA(x[np.index, ])/100

+cn.nonpolymorphic <- CA(obj, i=which(!isSnp(obj)))

 @ 

 Total copy number at both polymorphic and nonpolymorphic loci:

 <<totalCopynumber>>=

-cn <- copyNumber(x)

+##cn <- copyNumber(x)

+cn <- totalCopyNumber(x, sample(1:nrow(x), 1e4), 1:5)

 apply(cn, 2, median, na.rm=TRUE)

 @