| 97e84a80 | linearParamElementReplace <- function(obj, elt, value) {
|
| 6846d583 | storage.mode <- storageMode(batchStatistics(obj)) |
| 97e84a80 | switch(storage.mode,
"lockedEnvironment" = {
|
| 6846d583 | aData <- copyEnv(batchStatistics(obj)) |
| 97e84a80 | if (is.null(value)) rm(list=elt, envir=aData)
else aData[[elt]] <- value
Biobase:::assayDataEnvLock(aData)
|
| 6846d583 | batchStatistics(obj) <- aData |
| 97e84a80 | },
"environment" = {
|
| 6846d583 | if (is.null(value)) rm(list=elt, envir=batchStatistics(obj))
else batchStatistics(obj)[[elt]] <- value
|
| 97e84a80 | }, |
| 6846d583 | list = batchStatistics(obj)[[elt]] <- value) |
| 97e84a80 | obj } |
| 6846d583 | ## parameters |
| 97e84a80 | setMethod("nuA", signature=signature(object="CNSet"), function(object) nu(object, "A"))
setMethod("nuB", signature=signature(object="CNSet"), function(object) nu(object, "B"))
setMethod("phiA", signature=signature(object="CNSet"), function(object) phi(object, "A"))
setMethod("phiB", signature=signature(object="CNSet"), function(object) phi(object, "B"))
|
| 6846d583 | setMethod("phiPrimeA", signature=signature(object="CNSet"), function(object) {
assayDataElement(batchStatistics(object), "phiPrimeA")
})
setMethod("phiPrimeB", signature=signature(object="CNSet"), function(object) {
assayDataElement(batchStatistics(object), "phiPrimeB")
})
|
| 97e84a80 | setMethod("tau2A", signature=signature(object="CNSet"), function(object) tau2(object, "A"))
setMethod("tau2B", signature=signature(object="CNSet"), function(object) tau2(object, "B"))
|
| 6846d583 |
setMethod("Ns", signature=signature(object="CNSet"),
function(object, ...){
Ns(batchStatistics(object), ...)
})
setMethod("corr", signature=signature(object="CNSet"),
function(object, ...){
corr(batchStatistics(object), ...)
})
setMethod("medians", signature=signature(object="CNSet"),
function(object, ...){
medians(batchStatistics(object), ...)
})
setMethod("mads", signature=signature(object="CNSet"),
function(object, ...){
mads(batchStatistics(object), ...)
})
setMethod("tau2", signature=signature(object="CNSet"),
function(object, ...){
tau2(batchStatistics(object), ...)
})
##---------------------------------------------------------------------------
## Number of samples with Genotype AA, AB, or BB by batch
setMethod("N.AA", signature=signature(object="CNSet"), function(object){
assayDataElement(batchStatistics(object), "N.AA")
})
setMethod("N.AB", signature=signature(object="CNSet"), function(object){
assayDataElement(batchStatistics(object), "N.AB")
})
setMethod("N.BB", signature=signature(object="CNSet"), function(object){
assayDataElement(batchStatistics(object), "N.BB")
})
|
| 0198a9ad | |
| 6846d583 | setReplaceMethod("N.AA", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "N.AA", value)
})
setReplaceMethod("N.AB", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "N.AB", value)
})
setReplaceMethod("N.BB", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "N.BB", value)
})
##---------------------------------------------------------------------------
## median intensity by genotype cluster for each allele
##should we update the entire matrix rather than one column...
setMethod("medianA.AA", signature=signature(object="CNSet"), function(object) {
assayDataElement(batchStatistics(object), "medianA.AA")
})
setMethod("medianA.AB", signature=signature(object="CNSet"), function(object) {
assayDataElement(batchStatistics(object), "medianA.AB")
})
setMethod("medianA.BB", signature=signature(object="CNSet"), function(object) {
assayDataElement(batchStatistics(object), "medianA.BB")
})
setMethod("medianB.AA", signature=signature(object="CNSet"), function(object) {
assayDataElement(batchStatistics(object), "medianB.AA")
})
setMethod("medianB.AB", signature=signature(object="CNSet"), function(object) {
assayDataElement(batchStatistics(object), "medianB.AB")
})
setMethod("medianB.BB", signature=signature(object="CNSet"), function(object) {
assayDataElement(batchStatistics(object), "medianB.BB")
})
setReplaceMethod("medianA.AA", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "medianA.AA", value)
})
setReplaceMethod("medianA.AB", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "medianA.AB", value)
})
setReplaceMethod("medianA.BB", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "medianA.BB", value)
})
setReplaceMethod("medianB.AA", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "medianB.AA", value)
})
setReplaceMethod("medianB.AB", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "medianB.AB", value)
})
setReplaceMethod("medianB.BB", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "medianB.BB", value)
})
##---------------------------------------------------------------------------
## mad intensity by genotype cluster for each allele
setMethod("madA.AA", signature=signature(object="CNSet"), function(object) {
assayDataElement(batchStatistics(object), "madA.AA")
})
setMethod("madA.AB", signature=signature(object="CNSet"), function(object) {
assayDataElement(batchStatistics(object), "madA.AB")
})
setMethod("madA.BB", signature=signature(object="CNSet"), function(object) {
assayDataElement(batchStatistics(object), "madA.BB")
})
setMethod("madB.AA", signature=signature(object="CNSet"), function(object) {
assayDataElement(batchStatistics(object), "madB.AA")
})
setMethod("madB.AB", signature=signature(object="CNSet"), function(object) {
assayDataElement(batchStatistics(object), "madB.AB")
})
setMethod("madB.BB", signature=signature(object="CNSet"), function(object) {
assayDataElement(batchStatistics(object), "madB.BB")
})
setReplaceMethod("madA.AA", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "madA.AA", value)
})
setReplaceMethod("madA.AB", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "madA.AB", value)
})
setReplaceMethod("madA.BB", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "madA.BB", value)
})
setReplaceMethod("madB.AA", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "madB.AA", value)
})
setReplaceMethod("madB.AB", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "madB.AB", value)
})
setReplaceMethod("madB.BB", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "madB.BB", value)
})
##---------------------------------------------------------------------------
## mad of log(intensities) by genotype cluster for each allele
setMethod("tau2A.AA", signature=signature(object="CNSet"), function(object) {
assayDataElement(batchStatistics(object), "tau2A.AA")
})
setMethod("tau2A.BB", signature=signature(object="CNSet"), function(object) {
assayDataElement(batchStatistics(object), "tau2A.BB")
})
setMethod("tau2B.AA", signature=signature(object="CNSet"), function(object) {
assayDataElement(batchStatistics(object), "tau2B.AA")
})
setMethod("tau2B.BB", signature=signature(object="CNSet"), function(object) {
assayDataElement(batchStatistics(object), "tau2B.BB")
})
setReplaceMethod("tau2A.AA", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "tau2A.AA", value)
})
setReplaceMethod("tau2A.BB", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "tau2A.BB", value)
})
setReplaceMethod("tau2B.AA", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "tau2B.AA", value)
})
setReplaceMethod("tau2B.BB", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "tau2B.BB", value)
})
## correlation of log2A and log2B within each genotype cluster
setMethod("corrAA", signature=signature(object="CNSet"), function(object){
assayDataElement(batchStatistics(object), "corrAA")
})
setMethod("corrAB", signature=signature(object="CNSet"), function(object){
assayDataElement(batchStatistics(object), "corrAB")
})
setMethod("corrBB", signature=signature(object="CNSet"), function(object){
assayDataElement(batchStatistics(object), "corrBB")
})
setReplaceMethod("corrAA", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "corrAA", value)
})
setReplaceMethod("corrAB", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "corrAB", value)
})
setReplaceMethod("corrBB", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "corrBB", value)
})
setReplaceMethod("phiPrimeA", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "phiPrimeA", value)
})
setReplaceMethod("phiPrimeB", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "phiPrimeB", value)
})
##setMethod("mad.AA", signature=signature(object="CNSet"), function(object) mads(object, "AA"))
##setMethod("mad.AB", signature=signature(object="CNSet"), function(object) mads(object, "AB"))
##setMethod("mad.BB", signature=signature(object="CNSet"), function(object) mads(object, "BB"))
##
##setReplaceMethod("median.AA", signature=signature(object="CNSet", value="ff_or_matrix"),
## function(object, value){
## linearParamElementReplace(object, "median.AA", value)
## })
##setReplaceMethod("median.AB", signature=signature(object="CNSet", value="ff_or_matrix"),
## function(object, value){
## linearParamElementReplace(object, "median.AB", value)
## })
##setReplaceMethod("median.BB", signature=signature(object="CNSet", value="ff_or_matrix"),
## function(object, value){
## linearParamElementReplace(object, "median.BB", value)
## })
##setReplaceMethod("mad.AA", signature=signature(object="CNSet", value="ff_or_matrix"),
## function(object, value){
## linearParamElementReplace(object, "mad.AA", value)
## })
##setReplaceMethod("mad.AB", signature=signature(object="CNSet", value="ff_or_matrix"),
## function(object, value){
## linearParamElementReplace(object, "mad.AB", value)
## })
##setReplaceMethod("mad.BB", signature=signature(object="CNSet", value="ff_or_matrix"),
## function(object, value){
## linearParamElementReplace(object, "mad.BB", value)
## })
|
| 97e84a80 | |
| d08acba1 | setReplaceMethod("nuA", signature=signature(object="CNSet", value="ff_or_matrix"),
|
| 97e84a80 | function(object, value){
linearParamElementReplace(object, "nuA", value)
})
|
| d08acba1 | setReplaceMethod("nuB", signature=signature(object="CNSet", value="ff_or_matrix"),
|
| 97e84a80 | function(object, value){
|
| 69ec8644 | linearParamElementReplace(object, "nuB", value) |
| e40ceb44 | }) |
| d5bc779e | |
| d08acba1 | setReplaceMethod("phiA", signature=signature(object="CNSet", value="ff_or_matrix"),
|
| 97e84a80 | function(object, value){
|
| 69ec8644 | linearParamElementReplace(object, "phiA", value) |
| e40ceb44 | }) |
| d5bc779e | |
| d08acba1 | setReplaceMethod("phiB", signature=signature(object="CNSet", value="ff_or_matrix"),
|
| 97e84a80 | function(object, value){
|
| 69ec8644 | linearParamElementReplace(object, "phiB", value) |
| e409d4f2 | }) |
| d08acba1 | setReplaceMethod("tau2A", signature=signature(object="CNSet", value="ff_or_matrix"),
|
| 97e84a80 | function(object, value){
|
| 69ec8644 | linearParamElementReplace(object, "tau2A", value) |
| 97e84a80 | }) |
| d5bc779e | |
| d08acba1 | setReplaceMethod("tau2B", signature=signature(object="CNSet", value="ff_or_matrix"),
|
| 97e84a80 | function(object, value){
|
| 69ec8644 | linearParamElementReplace(object, "tau2B", value) |
| 97e84a80 | }) |
| d5bc779e | |
| 5fcfed7d | |
| 76f72a5a | |
| d08acba1 | setReplaceMethod("flags", signature=signature(object="CNSet", value="ff_or_matrix"),
function(object, value){
linearParamElementReplace(object, "flags", value)
})
|
| 6846d583 | setReplaceMethod("flags", signature=signature(object="CNSet", value="ff_matrix"),
function(object, value){
linearParamElementReplace(object, "flags", value)
})
|
| d08acba1 | |
| 97e84a80 | |
| 0198a9ad | ## allele A
## autosome SNPs
## autosome NPs
## chromosome X NPs for women
C1 <- function(object, marker.index, batch.index, sample.index){
|
| a268cdc3 | ## acn <- vector("list", length(batch.index))
acn <- matrix(NA, nrow=length(marker.index), ncol=length(sample.index))
|
| 0198a9ad | for(k in seq_along(batch.index)){
l <- batch.index[k]
jj <- sample.index[as.character(batch(object))[sample.index] == batchNames(object)[l]]
bg <- nuA(object)[marker.index, l]
slope <- phiA(object)[marker.index, l]
I <- A(object)[marker.index, jj]
|
| a268cdc3 | acn[, match(jj, sample.index)] <- 1/slope * (I - bg) |
| 0198a9ad | } |
| a268cdc3 | ## if(length(acn) > 1){
## acn <- do.call("cbind", acn)
## } else acn <- acn[[1]]
|
| 9568a401 | return(as.matrix(acn)) |
| 0198a9ad | } |
| 197c7911 | ## allele B (treated allele 'A' for chromosome X NPs) |
| 0198a9ad | ## autosome SNPs
## chromosome X for male nonpolymorphic markers
C2 <- function(object, marker.index, batch.index, sample.index, NP.X=FALSE){
|
| a268cdc3 | acn <- matrix(NA, nrow=length(marker.index), ncol=length(sample.index)) |
| 0198a9ad | for(k in seq_along(batch.index)){
l <- batch.index[k]
jj <- sample.index[as.character(batch(object))[sample.index] == batchNames(object)[l]]
bg <- nuB(object)[marker.index, l]
slope <- phiB(object)[marker.index, l]
if(!NP.X){
I <- B(object)[marker.index, jj]
} else I <- A(object)[marker.index, jj]
|
| a268cdc3 | acn[, match(jj, sample.index)] <- 1/slope * (I - bg) |
| 0198a9ad | } |
| a268cdc3 | ## if(length(acn) > 1){
## acn <- do.call("cbind", acn)
## } else acn <- acn[[1]]
|
| 9568a401 | return(as.matrix(acn)) |
| 0198a9ad | }
## Chromosome X SNPs
C3 <- function(object, allele, marker.index, batch.index, sample.index){
|
| a268cdc3 | ## acn <- vector("list", length(batch.index))
acn <- matrix(NA, nrow=length(marker.index), ncol=length(sample.index))
|
| 0198a9ad | for(k in seq_along(batch.index)){
l <- batch.index[k]
##j <- which(as.character(batch(object))[sample.index] == batchNames(object)[l])
jj <- sample.index[as.character(batch(object))[sample.index] == batchNames(object)[l]]
phiA2 <- phiPrimeA(object)[marker.index, l]
phiB2 <- phiPrimeB(object)[marker.index, l]
phiA <- phiA(object)[marker.index, l]
phiB <- phiB(object)[marker.index, l]
nuA <- nuA(object)[marker.index, l]
|
| 89c5fe95 | nuB <- nuB(object)[marker.index, l] |
| 0198a9ad | IA <- A(object)[marker.index, jj] IB <- B(object)[marker.index, jj] |
| 89c5fe95 | phistar <- phiB2/phiA tmp <- (IB - nuB - phistar*IA + phistar*nuA)/phiB CB <- tmp/(1-phistar*phiA2/phiB) ##CB <- 1/(1-phiA2*phiB2/(phiA*phiB)) * 1/phiB * (IA-nuB-phiB2/phiA*(IA-nuA)) CA <- (IA-nuA-phiA2*CB)/phiA |
| 0198a9ad | if(allele == "B"){
|
| a268cdc3 | acn[, match(jj, sample.index)] <- CB ##acn[[k]] <- CB |
| 0198a9ad | }
if(allele == "A"){
|
| a268cdc3 | acn[, match(jj, sample.index)] <- (IA-nuA-phiA2*CB)/phiA
}
if(allele == "AandB"){
CA <- tmp/(1-phistar*phiA2/phiB)
CB <- (IA-nuA-phiA2*CB)/phiA
acn[, match(jj, sample.index)] <- (IA-nuA-phiA2*CB)/phiA
|
| 0198a9ad | } |
| 89c5fe95 | ## if(allele=="AandB") ## CA <- tmp/(1-phistar*phiA2/phiB) ## CB <- (IA-nuA-phiA2*CB)/phiA ## acn[[k]] <- CA+CB ## } |
| 0198a9ad | } |
| a268cdc3 | ## if(length(acn) > 1){
## acn <- do.call("cbind", acn)
## } else acn <- acn[[1]]
|
| 9568a401 | return(as.matrix(acn)) |
| 0198a9ad | } |
| 8e2d9355 | |
| 0198a9ad | |
| 518a2908 | |
| 805ca33b | ACN <- function(object, allele, i , j){
|
| 6846d583 | if(missing(i) & missing(j)) stop("must specify rows (i) or columns (j)")
|
| 9568a401 | is.ff <- is(calls(object), "ff") | is(calls(object), "ffdf") |
| 0198a9ad | missing.i <- missing(i)
missing.j <- missing(j)
if(!missing.i){
is.ann <- !is.na(chromosome(object)[i])
is.X <- chromosome(object)[i]==23 & is.ann
is.auto <- chromosome(object)[i] < 23 & is.ann
is.snp <- isSnp(object)[i] & is.ann
} else{
is.ann <- !is.na(chromosome(object))
is.X <- chromosome(object)==23 & is.ann
is.auto <- chromosome(object) < 23 & is.ann
is.snp <- isSnp(object) & is.ann
i <- 1:nrow(object)
}
## Define batch.index and sample.index
if(!missing.j) {
batches <- unique(as.character(batch(object))[j])
|
| a268cdc3 | ##batches <- as.character(batch(object)[j]) |
| 0198a9ad | batch.index <- match(batches, batchNames(object))
} else {
batch.index <- seq_along(batchNames(object))
j <- 1:ncol(object)
}
nr <- length(i)
nc <- length(j)
acn <- matrix(NA, nr, nc)
|
| a268cdc3 | dimnames(acn) <- list(featureNames(object)[i], sampleNames(object)[j]) |
| 0198a9ad | if(allele == "A"){
if(is.ff){
open(nuA(object))
open(phiA(object))
open(A(object))
}
## --
## 4 types of markers for allele A
##--
## 1. autosomal SNPs or autosomal NPs
if(any(is.auto)){
auto.index <- which(is.auto)
marker.index <- i[is.auto]
acn[auto.index, ] <- C1(object, marker.index, batch.index, j)
}
if(any(is.X)){
##2. CHR X SNPs (men and women)
if(any(is.snp)){
if(is.ff) {
open(phiPrimeA(object))
open(phiPrimeB(object))
open(phiB(object))
open(nuB(object))
open(B(object))
}
marker.index <- i[is.X & is.snp]
acn.index <- which(is.X & is.snp)
acn[acn.index, ] <- C3(object, allele="A", marker.index, batch.index, j)
if(is.ff) {
close(phiPrimeA(object))
close(phiPrimeB(object))
close(phiB(object))
close(nuB(object))
close(B(object))
}
}
|
| a268cdc3 | if(any(!is.snp)){
|
| 0198a9ad | marker.index <- i[is.X & !is.snp] acn.index <- which(is.X & !is.snp) acn[acn.index, ] <- NA |
| 4191b5f9 | female.index <- j[object$gender[j] == 2]
## 3. CHR X NPs: women
if(length(female.index) > 0){
female.batch.index <- match(unique(as.character(batch(object))[female.index]), batchNames(object))
jj <- which(object$gender[j] == 2)
acn[acn.index, jj] <- C1(object, marker.index, female.batch.index, female.index)
}
|
| 0198a9ad | ## ## 4. CHR X NPs: men |
| 4191b5f9 | male.index <- j[object$gender[j] == 1]
if(length(male.index) > 0){
if(is.ff){
open(nuB(object))
open(phiB(object))
}
male.batch.index <- match(unique(as.character(batch(object))[male.index]), batchNames(object))
jj <- which(object$gender[j] == 1)
acn[acn.index, jj] <- C2(object, marker.index, male.batch.index, male.index, NP.X=TRUE)
if(is.ff){
close(nuB(object))
close(phiB(object))
}
}
|
| 6846d583 | } } |
| 0198a9ad | if(is.ff){
close(nuA(object))
close(phiA(object))
close(A(object))
|
| 805ca33b | } } |
| 0198a9ad | if(allele == "B"){
if(is.ff){
open(nuB(object))
open(phiB(object))
open(B(object))
|
| 805ca33b | } |
| a268cdc3 | if(any(!is.snp)){
acn.index <- which(!is.snp)
acn[acn.index, ] <- 0
}
|
| 89c5fe95 | if(any(is.auto)){
|
| 197c7911 | auto.index <- which(is.auto & is.snp)
if(length(auto.index) > 0){
|
| a268cdc3 | marker.index <- i[auto.index] |
| 197c7911 | acn[auto.index, ] <- C2(object, marker.index, batch.index, j) } |
| d5b39e21 | } |
| 89c5fe95 | if(any(is.X)){
##Chr X SNPs
if(any(is.snp)){
if(is.ff) {
|
| 0198a9ad | open(phiPrimeA(object)) open(phiPrimeB(object)) open(phiA(object)) open(nuA(object)) open(A(object)) } marker.index <- i[is.X & is.snp] acn.index <- which(is.X & is.snp) acn[acn.index, ] <- C3(object, allele="B", marker.index, batch.index, j) |
| 89c5fe95 | if(is.ff) {
|
| 0198a9ad | close(phiPrimeA(object)) close(phiPrimeB(object)) close(phiA(object)) close(nuA(object)) close(A(object)) } } |
| 89c5fe95 | if(any(!is.snp)){
acn.index <- which(!is.snp)
marker.index <- i[!is.snp]
acn[acn.index, ] <- 0
}
|
| 0198a9ad | } |
| f3738959 | }
if(is.ff){
close(nuB(object))
close(phiB(object))
close(B(object))
|
| 805ca33b | } return(acn) } |
| ddc94a58 | |
| 69ec8644 | setMethod("CA", signature=signature(object="CNSet"),
function(object, ...){
ca <- ACN(object, allele="A", ...)
|
| 0198a9ad | ca[ca < 0] <- 0 |
| 66900fea | ca[ca > 5] <- 5 |
| ddc94a58 | return(ca) |
| 2c958cfa | }) |
| 69ec8644 | setMethod("CB", signature=signature(object="CNSet"),
function(object, ...) {
cb <- ACN(object, allele="B", ...)
|
| 0198a9ad | cb[cb < 0] <- 0 |
| 66900fea | cb[cb > 5] <- 5 |
| 805ca33b | return(cb) }) |
| 752632c4 | |
| 6b75ec77 | setMethod("totalCopynumber", signature=signature(object="CNSet"),
function(object, ...){
|
| fda11070 | ca <- CA(object, ...) cb <- CB(object, ...) return(ca+cb) }) |
| 69ec8644 | |
| 97e84a80 | setReplaceMethod("snpCall", c("CNSet", "ff_or_matrix"),
function(object, ..., value){
assayDataElementReplace(object, "call", value)
})
|
| 66900fea | setReplaceMethod("snpCallProbability", c("CNSet", "ff_or_matrix"),
function(object, ..., value){
assayDataElementReplace(object, "callProbability", value)
})
|