Browse code

add scale.sd option to computePosteriorMeans

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@53848 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 18/03/2011 01:57:07
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@@ -71,10 +71,3 @@ export(constructIlluminaCNSet)
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 export(totalCopynumber, rawCopynumber)
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 exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)
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-## for posterior means
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-
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-##export(summarizeNps, genotypeSummary, fit.lm2)
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@@ -2290,6 +2290,15 @@ posteriorMean.snp <- function(stratum, object, index.list, CN,
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 		       cn3=4,
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 		       cn4=4,
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 		       cn5=6, NULL)
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+	}
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+	##emit <- vector("list", length(sample.index))
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+	for(j in seq_along(sample.index)){
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+		cat("batch ", j, "\n")
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+		J <- sample.index[[j]]
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+		probs <- array(NA, dim=c(nrow(a), length(J), S))
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+		for(k in seq_along(CN)){
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+			CT <- CN[k]
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+			## 5: AAAAA, AAAAB, AAABB, AABBB, ABBBB, BBBBB
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 			##CN=4
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 			## AAAA, AAAB, AABB, ABBB, BBBB:  L = 4
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 			##CN=3