@@ -57,7 +57,7 @@ importFrom(ff, ffdf, physical.ff, physical.ffdf)

 exportClasses(CNSetLM, ffdf, list)

 exportMethods(open, "[", show, lM, lines, nu, phi, corr, sigma2, tau2)

-exportMethods(CA, CB)

+exportMethods(CA, CB, totalCopyNumber)

 export(crlmm, 

        crlmmCopynumber, 

        crlmmIllumina, 

@@ -245,3 +245,41 @@ setMethod("CA", "CNSet", function(object) {

 	browser()

 	##assayDataElement(object, "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(missing(i) & !missing(j)){

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

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

+		if(length(snp.index) > 0){

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

+			snps <- (1:nrow(cn.total))[i %in% snp.index]

+			cn.total[snps, ] <- cn.total[snps, j] + cb				

+		}

+	}

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

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

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

+		if(length(snp.index) > 0){

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

+			snps <- (1:nrow(cn.total))[i %in% snp.index]

+			cn.total[snps, ] <- cn.total[snps, ] + cb				

+		}

+	}

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

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

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

+		if(length(snp.index) > 0){

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

+			snps <- (1:nrow(cn.total))[i %in% snp.index]

+			cn.total[snps, ] <- cn.total[snps, ] + cb

+		}

+	}

+	cn.total <- cn.total/100

+	dimnames(cn.total) <- NULL

+	return(cn.total)

+})