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Bug fix for calculateRTheta

should not use snp.index when retrieving the centers. Replace with seq_len(nrow(cnSet))

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58759 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 04/10/2011 16:11:40
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@@ -2766,7 +2766,8 @@ ABpanel <- function(x, y, predictRegion,
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 calculateRTheta <- function(cnSet, genotype=c("AA", "AB", "BB"), batch.name){
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 	genotype <- match.arg(genotype)
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 	j <- match(batch.name, batchNames(cnSet))
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-	centers <- medians(cnSet, i=snp.index, j)
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+	##centers <- medians(cnSet, i=snp.index, j)
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+	centers <- medians(cnSet, i=seq_len(nrow(cnSet)), j)
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 	theta <- matrix(NA, nrow(cnSet), 2)
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 	colnames(theta) <- c("theta", "R")
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 	x <- centers[, "A", genotype, 1]