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Edit crlmmCopynumber -- summarizeSnps only called for types SNP, NP, and X.NP

SNPs on chr X are summarized during fit.lm3 through the call to summarizeXGenotypes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52820 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 15:57:24
Showing1 changed files

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@@ -1392,7 +1392,7 @@ genotypeSummary <- function(object,
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 		switch(type,
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 		       SNP="summarizeSnps",
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 		       NP="summarizeNps",
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-		       X.SNP="summarizeSnps",
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+##		       X.SNP="summarizeSnps",
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 		       X.NP="summarizeNps")
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 	}
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 	myf <- summaryFxn(type[[1]])
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@@ -1650,12 +1650,9 @@ crlmmCopynumber <- function(object,
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 		       X.SNP="chromosome X SNPs",
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 		       X.NP="chromosome X nonpolymorphic markers")
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 	}
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-	if(verbose & is.lds) {
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-		message("Large data support with ff package is enabled.")
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-		message("To reduce RAM, the markers are divided into several strata (see ?ocProbesets for details) and summary statistics are computed on each stratum")
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-	}
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-	for(i in seq_along(type)){
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-		## do all types
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+	if(verbose) message("Computing summary statistics of the genotype clusters for each batch")
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+##	for(i in seq_along(type)){
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+	for(i in c(1, 2, 4)){ ## do not do X.SNP.  Do this during fit.lm3
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 		marker.type <- type[i]
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 		if(verbose) message(paste("...", mylabel(marker.type)))
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 		##if(verbose) message(paste("Computing summary statistics for ", mylabel(marker.type), " genotype clusters for each batch")