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
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@@ -57,16 +57,12 @@ setGeneric("madB.AB<-", function(object, value) standardGeneric("madB.AB<-"))
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| 57 | 57 |
setGeneric("madB.BB<-", function(object, value) standardGeneric("madB.BB<-"))
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| 58 | 58 |
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| 59 | 59 |
setGeneric("tau2A.AA", function(object) standardGeneric("tau2A.AA"))
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| 60 |
-##setGeneric("tau2A.AB", function(object) standardGeneric("tau2A.AB"))
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| 61 | 60 |
setGeneric("tau2A.BB", function(object) standardGeneric("tau2A.BB"))
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| 62 | 61 |
setGeneric("tau2B.AA", function(object) standardGeneric("tau2B.AA"))
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| 63 |
-##setGeneric("tau2B.AB", function(object) standardGeneric("tau2B.AB"))
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| 64 | 62 |
setGeneric("tau2B.BB", function(object) standardGeneric("tau2B.BB"))
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| 65 | 63 |
setGeneric("tau2A.AA<-", function(object, value) standardGeneric("tau2A.AA<-"))
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| 66 |
-##setGeneric("tau2A.AB<-", function(object, value) standardGeneric("tau2A.AB<-"))
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| 67 | 64 |
setGeneric("tau2A.BB<-", function(object, value) standardGeneric("tau2A.BB<-"))
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| 68 | 65 |
setGeneric("tau2B.AA<-", function(object, value) standardGeneric("tau2B.AA<-"))
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| 69 |
-##setGeneric("tau2B.AB<-", function(object, value) standardGeneric("tau2B.AB<-"))
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| 70 | 66 |
setGeneric("tau2B.BB<-", function(object, value) standardGeneric("tau2B.BB<-"))
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| 71 | 67 |
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| 72 | 68 |
setGeneric("corrAA", function(object) standardGeneric("corrAA"))
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| ... | ... |
@@ -86,16 +82,12 @@ setGeneric("phiPrimeA", function(object) standardGeneric("phiPrimeA"))
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| 86 | 82 |
setGeneric("phiPrimeB", function(object) standardGeneric("phiPrimeB"))
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| 87 | 83 |
setGeneric("phiPrimeA<-", function(object, value) standardGeneric("phiPrimeA<-"))
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| 88 | 84 |
setGeneric("phiPrimeB<-", function(object, value) standardGeneric("phiPrimeB<-"))
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| 89 |
-setGeneric("sigma2A", function(object) standardGeneric("sigma2A"))
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| 90 |
-setGeneric("sigma2B", function(object) standardGeneric("sigma2B"))
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| 91 | 85 |
setGeneric("tau2A", function(object) standardGeneric("tau2A"))
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| 92 | 86 |
setGeneric("tau2B", function(object) standardGeneric("tau2B"))
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| 93 | 87 |
setGeneric("nuA<-", function(object, value) standardGeneric("nuA<-"))
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| 94 | 88 |
setGeneric("nuB<-", function(object, value) standardGeneric("nuB<-"))
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| 95 | 89 |
setGeneric("phiA<-", function(object, value) standardGeneric("phiA<-"))
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| 96 | 90 |
setGeneric("phiB<-", function(object, value) standardGeneric("phiB<-"))
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| 97 |
-setGeneric("sigma2A<-", function(object, value) standardGeneric("sigma2A<-"))
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| 98 |
-setGeneric("sigma2B<-", function(object, value) standardGeneric("sigma2B<-"))
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| 99 | 91 |
setGeneric("tau2A<-", function(object, value) standardGeneric("tau2A<-"))
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| 100 | 92 |
setGeneric("tau2B<-", function(object, value) standardGeneric("tau2B<-"))
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| 101 | 93 |
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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| 27 | 27 |
setMethod("phiPrimeB", signature=signature(object="CNSet"), function(object) {
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| 28 | 28 |
assayDataElement(batchStatistics(object), "phiPrimeB") |
| 29 | 29 |
}) |
| 30 |
-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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| 32 | 30 |
setMethod("tau2A", signature=signature(object="CNSet"), function(object) tau2(object, "A"))
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| 33 | 31 |
setMethod("tau2B", signature=signature(object="CNSet"), function(object) tau2(object, "B"))
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| 34 | 32 |
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| ... | ... |
@@ -286,16 +284,6 @@ setReplaceMethod("phiB", signature=signature(object="CNSet", value="ff_or_matrix
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| 286 | 284 |
linearParamElementReplace(object, "phiB", value) |
| 287 | 285 |
}) |
| 288 | 286 |
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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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| 299 | 287 |
setReplaceMethod("tau2A", signature=signature(object="CNSet", value="ff_or_matrix"),
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| 300 | 288 |
function(object, value){
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| 301 | 289 |
linearParamElementReplace(object, "tau2A", value) |
| ... | ... |
@@ -20,10 +20,6 @@ linesCNSet <- function(x, y, batch, copynumber, x.axis="A", ...){
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| 20 | 20 |
tau2B <- taus[, "B", "AA", ] |
| 21 | 21 |
sigma2A <- taus[, "A", "AA", ] |
| 22 | 22 |
sigma2B <- taus[, "B", "BB", ] |
| 23 |
-## tau2A <- tau2(object, "A")[marker.index, batch.index] |
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| 24 |
-## tau2B <- tau2(object, "B")[marker.index, batch.index] |
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-## sigma2A <- sigma2(object, "A")[marker.index, batch.index] |
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| 26 |
-## sigma2B <- sigma2(object, "B")[marker.index, batch.index] |
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| 27 | 23 |
cors <- corr(object, i=marker.index, j=batch.index)[, , ] |
| 28 | 24 |
corrAB <- cors[["AB"]] |
| 29 | 25 |
corrAA <- cors[["AA"]] |