@@ -71,10 +71,3 @@ export(constructIlluminaCNSet)

 export(totalCopynumber, rawCopynumber)

 exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)

-## for posterior means

-

-

-

-

-

-##export(summarizeNps, genotypeSummary, fit.lm2)

@@ -2290,6 +2290,15 @@ posteriorMean.snp <- function(stratum, object, index.list, CN,

 		       cn3=4,

 		       cn4=4,

 		       cn5=6, NULL)

+	}

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

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

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

+		J <- sample.index[[j]]

+		probs <- array(NA, dim=c(nrow(a), length(J), S))

+		for(k in seq_along(CN)){

+			CT <- CN[k]

+			## 5: AAAAA, AAAAB, AAABB, AABBB, ABBBB, BBBBB

 			##CN=4

 			## AAAA, AAAB, AABB, ABBB, BBBB:  L = 4

 			##CN=3