Browse code

Changed generic for CA and CB to include index i for markers and index j for samples

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48939 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:48:17
Showing2 changed files

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@@ -16,8 +16,8 @@ setGeneric("phi", function(object, allele) standardGeneric("phi"))
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 setGeneric("sigma2", function(object, allele) standardGeneric("sigma2"))
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 setGeneric("tau2", function(object, allele) standardGeneric("tau2"))
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-setGeneric("CA", function(object) standardGeneric("CA"))
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-setGeneric("CB", function(object) standardGeneric("CB"))
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+setGeneric("CA", function(object, i, j, ...) standardGeneric("CA"))
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+setGeneric("CB", function(object, i, j, ...) standardGeneric("CB"))
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 setGeneric("totalCopyNumber", function(object, i, j, ...) standardGeneric("totalCopyNumber"))
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@@ -237,14 +237,17 @@ setMethod("corr", c("CNSetLM", "character"), function(object, allele){
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 	return(res)
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 })
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-setMethod("CB", "CNSet", function(object){
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-	##assayDataElement(object, "CB")
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-	browser()
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-})
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-setMethod("CA", "CNSet", function(object) {
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-	browser()
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-	##assayDataElement(object, "CA")
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-})
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+setMethod("CB", 
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+	  signature=signature(object="CNSet", i="integerOrMissing", j="integerOrMissing"),
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+	  function(object, i, j){
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+		  ##assayDataElement(object, "CB")
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+		  browser()
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+	  })
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+setMethod("CA",
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+	  signature=signature(object="CNSet", i="integerOrMissing", j="integerOrMissing"),
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+	  function(object, i, j) {
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+		  browser()
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+	  })
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 setMethod("totalCopyNumber",
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 	  signature=signature(object="CNSet", i="integerOrMissing", j="integerOrMissing"),