@@ -1,7 +1,7 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

-Version: 1.7.9

+Version: 1.7.11

 Date: 2010-07-30

 Author: Rafael A Irizarry, Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>

 Maintainer: Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

@@ -50,8 +50,8 @@ setAs("SnpSuperSet", "CNSetLM", function(from, to){

 		     alleleB=B(from),

 		     call=snpCall(from),

 		     callProbability=snpCallProbability(from),

-		     CA=initializeBigMatrix("CA", nrow(from), ncol(from)),

-		     CB=initializeBigMatrix("CB", nrow(from), ncol(from)),

+##		     CA=initializeBigMatrix("CA", nrow(from), ncol(from)),

+##		     CB=initializeBigMatrix("CB", nrow(from), ncol(from)),

 		     annotation=annotation(from),

 		     featureData=featureData(from),

 		     experimentData=experimentData(from),

@@ -105,24 +105,6 @@ setMethod("computeCopynumber", "CNSet",

 	object

 })

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

-	I <- isSnp(object)

-	ffIsLoaded <- class(calls(object))[[1]]=="ff"

-	CA <- CA(object)

-	CB <- CB(object)

-	if(ffIsLoaded){

-		open(CA)

-		open(CB)

-		CA <- as.matrix(CA[,])

-		CB <- as.matrix(CB[,])

-	}

-	CN <- CA + CB

-	##For nonpolymorphic probes, CA is the total copy number

-	CN[!I, ] <- CA(object)[!I, ]

-	CN <- CN/100

-	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")

@@ -150,58 +132,10 @@ setMethod("totalCopyNumber", "CNSet", function(object, i, j){

 	return(cn.total)

 })

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

-##	I <- isSnp(object)

-##	CA <- CA(object)

-##	CB <- CB(object)

-##	CN <- CA + CB

-##	##For nonpolymorphic probes, CA is the total copy number

-##	CN[!I, ] <- CA(object)[!I, ]

-##	CN

-##})

-

-

 setMethod("ellipse", "CNSet", function(x, copynumber, batch, ...){

 	ellipse.CNSet(x, copynumber, batch, ...)

 })

-##setMethod("ellipse", "CNSet", function(x, copynumber, ...){

-ellipse.CNSet <- function(x, copynumber, batch, ...){

-	if(nrow(x) > 1) stop("only 1 snp at a time")

-	##batch <- unique(x$batch)

-	if(missing(batch)){

-		stop("must specify batch")

-	}

-	if(length(batch) > 1) stop("batch variable not unique")

-	nuA <- getParam(x, "nuA", batch)

-	nuB <- getParam(x, "nuB", batch)

-	phiA <- getParam(x, "phiA", batch)

-	phiB <- getParam(x, "phiB", batch)

-	tau2A <- getParam(x, "tau2A", batch)

-	tau2B <- getParam(x, "tau2B", batch)

-	sig2A <- getParam(x, "sig2A", batch)

-	sig2B <- getParam(x, "sig2B", batch)

-	corrA.BB <- getParam(x, "corrA.BB", batch)

-	corrB.AA <- getParam(x, "corrB.AA", batch)

-	corr <- getParam(x, "corr", batch)

-	for(CN in copynumber){

-		for(CA in 0:CN){

-			CB <- CN-CA

-			A.scale <- sqrt(tau2A*(CA==0) + sig2A*(CA > 0))

-			B.scale <- sqrt(tau2B*(CB==0) + sig2B*(CB > 0))

-			scale <- c(A.scale, B.scale)

-			if(CA == 0 & CB > 0) rho <- corrA.BB

-			if(CA > 0 & CB == 0) rho <- corrB.AA

-			if(CA > 0 & CB > 0) rho <- corr

-			if(CA == 0 & CB == 0) rho <- 0

-			lines(ellipse(x=rho, centre=c(log2(nuA+CA*phiA),

-					     log2(nuB+CB*phiB)),

-				      scale=scale), ...)

-		}

-	}

-}

-

-

 setMethod("nu", c("CNSetLM", "character"), function(object, allele){

 	getValue <- function(allele){

 		switch(allele,