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Commented code in summarizeSnps.

## if(CHR.X) {
## sample.index <- which(object$gender==2)
## batches <- split(sample.index, as.character(batch(object))[sample.index])
## } else {
## batches <- split(seq_along(batch(object)), as.character(batch(object)))
## }

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52814 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 15:57:01
Showing1 changed files

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@@ -1430,12 +1430,13 @@ summarizeSnps <- function(strata,
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 	}
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 	if(verbose) message("Probe stratum ", strata, " of ", length(index.list))
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 	index <- index.list[[strata]]
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-	if(CHR.X) {
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-		sample.index <- which(object$gender==2)
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-		batches <- split(sample.index, as.character(batch(object))[sample.index])
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-	} else {
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-		batches <- split(seq_along(batch(object)), as.character(batch(object)))
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-	}
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+##	if(CHR.X) {
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+##		sample.index <- which(object$gender==2)
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+##		batches <- split(sample.index, as.character(batch(object))[sample.index])
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+##	} else {
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+##		batches <- split(seq_along(batch(object)), as.character(batch(object)))
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+##	}
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+	batches <- split(seq_along(batch(object)), as.character(batch(object)))
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 	batchnames <- batchNames(object)
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 	nr <- length(index)
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 	nc <- length(batchnames)