@@ -10,3 +10,5 @@ Rprof*

 testing*

 sample.CNSetLMff.rda

 extdata*

+Makefile

+.Rhistory

@@ -447,32 +447,7 @@ setMethod("copyNumber", "CNSet", function(object){

 	CN

 })

-setMethod("totalCopyNumber", "CNSet", 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(missing(i) & !missing(j)){

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

-		cn.total <- as.matrix(CA(cnSet)[, j])

-		cb <- as.matrix(CB(cnSet)[snp.index, j]	)

-		cn.total[snp.index, ] <- cn.total[snp.index, ] + cb		

-	}

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

-		snp.index <- intersect(which(isSnp(object)), i)

-		cn.total <- as.matrix(CA(cnSet)[i, ])

-		cb <- as.matrix(CB(cnSet)[snp.index, ])	

-		cn.total[snp.index, ] <- cn.total[snp.index, ] + cb				

-	}

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

-		snp.index <- intersect(which(isSnp(object)), i)		

-		cn.total <- as.matrix(CA(cnSet)[i, j])	

-		cb <- as.matrix(CB(cnSet)[snp.index, j])

-		cn.total[snp.index, ] <- cn.total[snp.index, ] + cb

-	}

-	cn.total <- cn.total/100

-	dimnames(cn.total) <- NULL

-	return(cn.total)

-})

+

 ##setMethod("copyNumber", "CNSet", function(object){

 ##	I <- isSnp(object)