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update calculateRTheta so that NP probes have non-missing 'R' values

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@59941 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/11/2011 16:31:31
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@@ -2776,6 +2776,8 @@ calculateRTheta <- function(cnSet, genotype=c("AA", "AB", "BB"), batch.name){
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 	x[x < 64] <- 64
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 	y[y < 64] <- 64
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 	theta[, "theta"] <- atan2(y, x)*2/pi
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+	## so that 'R' is available for NP probes
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+	y[is.na(y)] <- 0
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 	theta[, "R"] <- x+y
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 	return(theta)
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 }
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Binary files a/data/cnSetExample.rda and b/data/cnSetExample.rda differ
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Binary files a/data/cnSetExample2.rda and b/data/cnSetExample2.rda differ