Browse code

Renamed computeCN crlmmCopynumber

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48956 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:49:37
Showing1 changed files

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@@ -761,16 +761,13 @@ crlmmCopynumberLD <- function(object,
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 		 neededPkgs="crlmm")
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 	return(object)
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 }
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-crlmmCopynumber <- crlmmCopynumber2 <- crlmmCopynumberLD
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+yycrlmmCopynumber2 <- crlmmCopynumberLD
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 fit.lm1 <- function(idxBatch,
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 		    snpBatches,
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-##		    autosomeIndex,
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 		    marker.index,
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 		    object,
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 		    Ns,
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-##		    normal,
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-##		    snpflags,
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 		    batchSize,
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 		    SNRMin,
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 		    MIN.SAMPLES,
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@@ -977,8 +974,6 @@ fit.lm2 <- function(idxBatch,
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 		    marker.index,
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 		    object,
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 		    Ns,
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-##		    normal,
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-##		    snpflags,
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 		    batchSize,
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 		    SNRMin,
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 		    MIN.SAMPLES,
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@@ -1088,8 +1083,6 @@ fit.lm3 <- function(idxBatch,
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 		    marker.index,
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 		    object,
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 		    Ns,
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-##		    normal,
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-##		    snpflags,
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 		    batchSize,
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 		    SNRMin,
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 		    MIN.SAMPLES,
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@@ -1327,8 +1320,6 @@ fit.lm4 <- function(idxBatch,
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 		    marker.index,
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 		    object,
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 		    Ns,
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-##		    normal,
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-##		    snpflags,
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 		    batchSize,
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 		    SNRMin,
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 		    MIN.SAMPLES,
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@@ -2774,9 +2765,9 @@ ellipseCenters <- function(object, index, allele, batch, log.it=TRUE){
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 }
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-computeCN <- function(object,
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-		      filenames,
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-		      which.batches,
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+crlmmCopynumber <- function(object,
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+			    filenames,
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+			    which.batches,
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 		      MIN.SAMPLES=10,
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 		      SNRMin=5,
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 		      MIN.OBS=1,