## Method("initialize", "AlleleSet",
## function(.Object,
## assayData = assayDataNew(alleleA=alleleA,
## alleleB=alleleB, ...),
## phenoData = annotatedDataFrameFrom(assayData, byrow=FALSE),
## featureData = annotatedDataFrameFrom(assayData, byrow=TRUE),
## experimentData = new("MIAME"),
## annotation = character(),
## protocolData = phenoData[,integer(0)],
## alleleA = new("matrix"),
## alleleB = matrix(numeric(),
## nrow=nrow(alleleA), ncol=ncol(alleleA),
## dimnames=dimnames(alleleA)),
## chromosome=integer(),
## position=integer(),
## isSnp=integer(),
## ...) {
## .Object <- callNextMethod(.Object,
## assayData = assayData,
## phenoData = phenoData,
## featureData = featureData,
## experimentData = experimentData,
## annotation = annotation,
## protocolData = protocolData)
## if(length(annotation) < 1){
## if((length(position) < 1 | length(chromosome) < 1| length(isSnp) < 1)){
## stop("must specify annotation if 'chromosome', 'position', and 'isSnp' are missing")
## } else {
## pData(featureData)$chromosome <- chromosome
## pData(featureData)$position <- position
## pData(featureData)$isSnp <- isSnp
## }
## } else{
## .Object@annotation <- annotation
## if((length(position) < 1 | length(chromosome) < 1| length(isSnp) < 1)){
## if(!isSupportedAnnotation(annotation)){
## stop("The annotation is not supported. Arguments 'chromosome', 'position', and 'isSnp' can be omitted from the initialization only if the annotation is supported (see oligoClasses:::supportedAnnotation()).")
## }
## } else {
## pData(featureData)$chromosome <- chromosome
## pData(featureData)$position <- position
## pData(featureData)$isSnp <- isSnp
## }
## .Object@featureData <- featureData
## }
## ## Do after annotation has been assigned
## if(!(all(c("chromosome", "position", "isSnp") %in% varLabels(featureData))) & isSupportedAnnotation(annotation)){
## ##update the featureData
## .Object@featureData <- addFeatureAnnotation.crlmm(.Object)
## }
## .Object
## })
##
## ow to make the initialization platform-specific?
## Method("initialize", "SnpSuperSet",
## function(.Object,
## call=new("matrix"),
## callProbability=matrix(NA, nrow(call), ncol(call), dimnames=dimnames(call)),
## phenoData = annotatedDataFrameFrom(assayData, byrow=FALSE),
## featureData=annotatedDataFrameFrom(assayData, byrow=TRUE),
## experimentData=new("MIAME"),
## annotation=character(),
## protocolData=phenoData[, integer(0)],
## position=integer(),
## chromosome=integer(),
## isSnp=integer(),...){
## .Object <- callNextMethod(.Object,
## call=call,
## callProbability=callProbability,
## phenoData=phenoData,
## featureData=featureData,
## experimentData=experimentData,
## annotation=annotation,
## protocolData=protocolData,
## position=position,
## chromosome=chromosome,
## isSnp=isSnp, ...)
## })
##
##setMethod("initialize", "SnpSuperSet",
## function(.Object,
## call=new("matrix"),
## callProbability=matrix(NA, nrow(call), ncol(call), dimnames=dimnames(call)),
## alleleA = new("matrix"),
## alleleB = matrix(numeric(),
## nrow=nrow(alleleA), ncol=ncol(alleleA),
## dimnames=dimnames(alleleA)),
## phenoData = annotatedDataFrameFrom(call, byrow=FALSE),
## featureData=annotatedDataFrameFrom(call, byrow=TRUE),
## experimentData=new("MIAME"),
## protocolData=phenoData[, integer(0)],
## position=integer(),
## chromosome=integer(),
## isSnp=integer(),
## annotation=character(), ... ){
## ##browser()
## ##the ... should be additional assayDataElements, if any
## .Object <- callNextMethod(.Object,
## call=call,
## callProbability=callProbability,
## alleleA=alleleA,
## alleleB=alleleB,
## phenoData=phenoData,
## featureData=featureData,
## experimentData=experimentData,
## protocolData=protocolData,
## annotation=annotation, ...)
## annotation <- .Object@annotation
## ##add chromosome, position, isSnp to featureData
## if(length(annotation) < 1){
## if((length(position) < 1| length(chromosome) < 1 | length(isSnp) < 1)){
## stop("must specify annotation if 'chromosome', 'position', and 'isSnp' are missing")
## } else {
## pData(featureData)$chromosome <- chromosome
## pData(featureData)$position <- position
## pData(featureData)$isSnp <- isSnp
## }
## } else{
## if((length(position) < 1| length(chromosome) < 1 | length(isSnp) < 1)){
## if(!isSupportedAnnotation(annotation)){
## stop("The annotation is not supported. Arguments 'chromosome', 'position', and 'isSnp' can be omitted from the initialization only if the annotation is supported (see oligoClasses:::supportedAnnotation()).")
## }
## } else {
## pData(featureData)$chromosome <- chromosome
## pData(featureData)$position <- position
## pData(featureData)$isSnp <- isSnp
## }
## .Object@featureData <- featureData
## }
## ##Do after annotation has been assigned
## if(!(all(c("chromosome", "position", "isSnp") %in% varLabels(featureData))) & isSupportedAnnotation(annotation)){
## .Object@featureData <- addFeatureAnnotation.crlmm(.Object)
## }
## .Object
## })
##setMethod("addFeatureAnnotation", "SnpSuperSet", function(object, ...){
## addFeatureAnnotation.crlmm(object, ...)
##})
##getParam.SnpSuperSet <- function(object, name, batch){
## label <- paste(name, batch, sep="_")
## colindex <- grep(label, fvarLabels(object))
## if(length(colindex) == 1){
## param <- fData(object)[, colindex]
## }
## if(length(colindex) < 1){
## param <- NULL
## }
## if(is.na(colindex)){
## stop(paste(label, " not found in object"))
## }
## if(length(colindex) > 1){
## stop(paste(label, " not unique"))
## }
## return(param)
## }
##setMethod("splitByChromosome", "SnpSuperSet", function(object, cnOptions){
## tmpdir <- cnOptions[["tmpdir"]]
## outdir <- cnOptions[["outdir"]]
## save.it <- cnOptions[["save.it"]]
## path <- system.file("extdata", package=paste(annotation(object), "Crlmm", sep=""))
## load(file.path(path, "snpProbes.rda"))
## snpProbes <- get("snpProbes")
## load(file.path(path, "cnProbes.rda"))
## cnProbes <- get("cnProbes")
## k <- grep("chr", colnames(snpProbes))
## if(length(k) < 1) stop("chr or chromosome not in colnames(snpProbes)")
## for(CHR in 1:24){
## cat("Chromosome ", CHR, "\n")
## snps <- rownames(snpProbes)[snpProbes[, k] == CHR]
## cnps <- rownames(cnProbes)[cnProbes[, k] == CHR]
## index <- c(match(snps, featureNames(object)),
## match(cnps, featureNames(object)))
## index <- index[!is.na(index)]
## callSetPlus <- object[index, ]
## if(CHR != 24){
## cnSet <- computeCopynumber(callSetPlus, cnOptions)
##
## } else{
## message("Copy number estimates not available for chromosome Y. Saving only the 'callSetPlus' object for this chromosome")
## save(callSetPlus, file=file.path(outdir, paste("callSetPlus_", CHR, ".rda", sep="")))
## }
## if(cnOptions[["hiddenMarkovModel"]] & CHR != 24){
## cnSet <- computeHmm(cnSet, cnOptions)
## }
## save(cnSet, file=file.path(outdir, paste("cnSet_", CHR, ".rda", sep="")))
## saved.objects <- list.files(outdir, pattern="cnSet", full.names=TRUE)
#### } else{ ## save crlmmSet to outdir
#### save(cnSet, file=file.path(outdir, paste("cnSet_", CHR, ".rda", sep="")))
#### saved.objects <- list.files(outdir, pattern="cnSet", full.names=TRUE)
#### }
## }
## saved.objects
##})
##setMethod("computeCopynumber", "SnpSuperSet",
## function(object, cnOptions){
## computeCopynumber.SnpSuperSet(object, cnOptions)
## })
