Browse code

removed generics and methods for sigma2A and sigma2B

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49141 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:41:06
Showing3 changed files

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@@ -57,16 +57,12 @@ setGeneric("madB.AB<-", function(object, value) standardGeneric("madB.AB<-"))
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 setGeneric("madB.BB<-", function(object, value) standardGeneric("madB.BB<-"))
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 setGeneric("tau2A.AA", function(object) standardGeneric("tau2A.AA"))
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-##setGeneric("tau2A.AB", function(object) standardGeneric("tau2A.AB"))
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 setGeneric("tau2A.BB", function(object) standardGeneric("tau2A.BB"))
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 setGeneric("tau2B.AA", function(object) standardGeneric("tau2B.AA"))
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-##setGeneric("tau2B.AB", function(object) standardGeneric("tau2B.AB"))
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 setGeneric("tau2B.BB", function(object) standardGeneric("tau2B.BB"))
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 setGeneric("tau2A.AA<-", function(object, value) standardGeneric("tau2A.AA<-"))
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-##setGeneric("tau2A.AB<-", function(object, value) standardGeneric("tau2A.AB<-"))
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 setGeneric("tau2A.BB<-", function(object, value) standardGeneric("tau2A.BB<-"))
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 setGeneric("tau2B.AA<-", function(object, value) standardGeneric("tau2B.AA<-"))
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-##setGeneric("tau2B.AB<-", function(object, value) standardGeneric("tau2B.AB<-"))
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 setGeneric("tau2B.BB<-", function(object, value) standardGeneric("tau2B.BB<-"))
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 setGeneric("corrAA", function(object) standardGeneric("corrAA"))
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@@ -86,16 +82,12 @@ setGeneric("phiPrimeA", function(object) standardGeneric("phiPrimeA"))
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 setGeneric("phiPrimeB", function(object) standardGeneric("phiPrimeB"))
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 setGeneric("phiPrimeA<-", function(object, value) standardGeneric("phiPrimeA<-"))
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 setGeneric("phiPrimeB<-", function(object, value) standardGeneric("phiPrimeB<-"))
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-setGeneric("sigma2A", function(object) standardGeneric("sigma2A"))
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-setGeneric("sigma2B", function(object) standardGeneric("sigma2B"))
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 setGeneric("tau2A", function(object) standardGeneric("tau2A"))
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 setGeneric("tau2B", function(object) standardGeneric("tau2B"))
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 setGeneric("nuA<-", function(object, value) standardGeneric("nuA<-"))
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 setGeneric("nuB<-", function(object, value) standardGeneric("nuB<-"))
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 setGeneric("phiA<-", function(object, value) standardGeneric("phiA<-"))
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 setGeneric("phiB<-", function(object, value) standardGeneric("phiB<-"))
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-setGeneric("sigma2A<-", function(object, value) standardGeneric("sigma2A<-"))
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-setGeneric("sigma2B<-", function(object, value) standardGeneric("sigma2B<-"))
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 setGeneric("tau2A<-", function(object, value) standardGeneric("tau2A<-"))
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 setGeneric("tau2B<-", function(object, value) standardGeneric("tau2B<-"))
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 setGeneric("flags<-", function(object, value) standardGeneric("flags<-"))
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@@ -27,8 +27,6 @@ setMethod("phiPrimeA", signature=signature(object="CNSet"), function(object) {
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 setMethod("phiPrimeB", signature=signature(object="CNSet"), function(object) {
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 	assayDataElement(batchStatistics(object), "phiPrimeB")
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 })
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-setMethod("sigma2A", signature=signature(object="CNSet"), function(object) sigma2(object, "A"))
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-setMethod("sigma2B", signature=signature(object="CNSet"), function(object) sigma2(object, "B"))
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 setMethod("tau2A", signature=signature(object="CNSet"), function(object) tau2(object, "A"))
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 setMethod("tau2B", signature=signature(object="CNSet"), function(object) tau2(object, "B"))
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@@ -286,16 +284,6 @@ setReplaceMethod("phiB", signature=signature(object="CNSet", value="ff_or_matrix
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 		  linearParamElementReplace(object, "phiB", value)
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 })
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-setReplaceMethod("sigma2A", signature=signature(object="CNSet", value="ff_or_matrix"),
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-	  function(object, value){
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-		  linearParamElementReplace(object, "sig2A", value)
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-})
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-
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-setReplaceMethod("sigma2B", signature=signature(object="CNSet", value="ff_or_matrix"),
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-	  function(object, value){
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-		  linearParamElementReplace(object, "sig2B", value)
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-})
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-
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 setReplaceMethod("tau2A", signature=signature(object="CNSet", value="ff_or_matrix"),
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 	  function(object, value){
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 		  linearParamElementReplace(object, "tau2A", value)
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@@ -20,10 +20,6 @@ linesCNSet <- function(x, y, batch, copynumber, x.axis="A", ...){
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 	tau2B <- taus[, "B", "AA", ]
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 	sigma2A <- taus[, "A", "AA", ]
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 	sigma2B <- taus[, "B", "BB", ]
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-##	tau2A <- tau2(object, "A")[marker.index, batch.index]
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-##	tau2B <- tau2(object, "B")[marker.index, batch.index]
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-##	sigma2A <- sigma2(object, "A")[marker.index, batch.index]
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-##	sigma2B <- sigma2(object, "B")[marker.index, batch.index]
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 	cors <- corr(object, i=marker.index, j=batch.index)[, , ]
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 	corrAB <- cors[["AB"]]
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 	corrAA <- cors[["AA"]]