@@ -2475,7 +2475,14 @@ calculatePosteriorMean <- function(object, type=c("SNP", "NP", "X.SNP", "X.NP"),

 	#}

 	} else stop("type not available")

-	if(length(emit)==1) emit <- emit[[1]] else stop("need to rbind elements of emit list?")

+	if(length(emit)==1) emit <- emit[[1]] else {

+		tmp <- array(NA, dim=c(length(unlist(marker.list)), ncol(object), length(prior.prob)))

+		for(i in seq_along(marker.list)){

+			marker.index <- marker.list[[i]]

+			tmp[marker.index, , ] <- emit[[i]]

+		}

+		emit <- tmp

+	}#stop("need to rbind elements of emit list?")

 	##tmp <- do.call("rbind", emit)

 	match.index <- match(rownames(emit), featureNames(object))

 	S <- length(prior.prob)

@@ -2485,14 +2492,7 @@ calculatePosteriorMean <- function(object, type=c("SNP", "NP", "X.SNP", "X.NP"),

 	return(object)

 }

-posteriorMean.snp <- function(stratum, object, index.list, CN,

-			      prior.prob=c(1/7, 1/7, 3/7, 1/7, 1/7), is.lds=TRUE, verbose=TRUE,

-			      scale.sd=1){

-	if(length(scale.sd) == 1) rep(scale.sd,2)

-	if(verbose) message("Probe stratum ", stratum, " of ", length(index.list))

-	index <- index.list[[stratum]]

-	test <- tryCatch(open(A(object)), error=function(e) NULL)

-	if(!is.null(test)){

+.open <- function(object){

 		open(B(object))

 		open(tau2A.AA(object))

 		open(tau2B.BB(object))

@@ -2505,7 +2505,47 @@ posteriorMean.snp <- function(stratum, object, index.list, CN,

 		open(nuB(object))

 		open(phiA(object))

 		open(phiB(object))

-	}

+}

+.close <- function(object){

+	close(A(object))

+	close(B(object))

+	close(tau2A.AA(object))

+	close(tau2B.BB(object))

+	close(tau2A.BB(object))

+	close(tau2B.AA(object))

+	close(corrAA(object))

+	close(corrAB(object))

+	close(corrBB(object))

+	close(nuA(object))

+	close(nuB(object))

+	close(phiA(object))

+	close(phiB(object))

+}

+

+sum.mymatrix <- function(...){

+	x <- list(...)

+	return(x[[1]] + do.call(sum, x[-1]))

+}

+numberGenotypes <- function(CT){

+	stopifnot(length(CT)==1)

+	copynumber <- paste("cn", CT, sep="")

+	switch(copynumber,

+		cn0=1,

+		cn1=2,

+		cn2=3,

+		cn3=4,

+		cn4=4,

+		cn5=6, NULL)

+}

+

+posteriorMean.snp <- function(stratum, object, index.list, CN,

+			      prior.prob=c(1/7, 1/7, 3/7, 1/7, 1/7), is.lds=TRUE, verbose=TRUE,

+			      scale.sd=1){

+	if(length(scale.sd) == 1) rep(scale.sd,2)

+	if(verbose) message("Probe stratum ", stratum, " of ", length(index.list))

+	index <- index.list[[stratum]]

+	test <- tryCatch(open(A(object)), error=function(e) NULL)

+	if(!is.null(test)) .open(object)

 	a <- log2(as.matrix(A(object)[index, ]))

 	b <- log2(as.matrix(B(object)[index, ]))

 	NN <- Ns(object, i=index)[, , 1]

@@ -2520,39 +2560,10 @@ posteriorMean.snp <- function(stratum, object, index.list, CN,

 	phiA <- as.matrix(phiA(object)[index, ])

 	nuB <- as.matrix(nuB(object)[index, ])

 	phiB <- as.matrix(phiB(object)[index, ])

-	if(!is.null(test)){

-		close(A(object))

-		close(B(object))

-		close(tau2A.AA(object))

-		close(tau2B.BB(object))

-		close(tau2A.BB(object))

-		close(tau2B.AA(object))

-		close(corrAA(object))

-		close(corrAB(object))

-		close(corrBB(object))

-		close(nuA(object))

-		close(nuB(object))

-		close(phiA(object))

-		close(phiB(object))

-	}

+	if(!is.null(test)) .close(object)

 	S <- length(prior.prob)

 	emit <- array(NA, dim=c(nrow(a), ncol(a), S))##SNPs x sample x 'truth'

 	sample.index <- split(1:ncol(object), batch(object))

-	sum.mymatrix <- function(...){

-		x <- list(...)

-		return(x[[1]] + do.call(sum, x[-1]))

-	}

-	numberGenotypes <- function(CT){

-		stopifnot(length(CT)==1)

-		copynumber <- paste("cn", CT, sep="")

-		switch(copynumber,

-		       cn0=1,

-		       cn1=2,

-		       cn2=3,

-		       cn3=4,

-		       cn4=4,

-		       cn5=6, NULL)

-	}

 	##emit <- vector("list", length(sample.index))

 	for(j in seq_along(sample.index)){

 		cat("batch ", j, "\n")

@@ -2577,10 +2588,11 @@ posteriorMean.snp <- function(stratum, object, index.list, CN,

 				CB <- CT-CA

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

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

-				if(CA == 0 | CB == 0){

+				if(CA == 0 | CB == 0){## possibly homozygous BB and AA, respectively

 					A.scale <- A.scale*scale.sd[1]

 					B.scale <- B.scale*scale.sd[1]

 				} else { ## one or both greater than zero

+					if(length(scale.sd) == 1) scale.sd <- rep(scale.sd, 2)

 					A.scale <- A.scale*scale.sd[2]

 					B.scale <- B.scale*scale.sd[2]

 				}