R/SegmentationDataFile.R

In HenrikBengtsson/aroma.core: Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

setConstructorS3("SegmentationDataFile", function(...) {
  extend(GenericDataFile(...), c("SegmentationDataFile"
                                        , uses("FileCacheKeyInterface")))
}, abstract=TRUE)


setMethodS3("getChromosome", "SegmentationDataFile", function(this, ..., force=FALSE) {
  chromosome <- this$.chromosome

  if (force || is.null(chromosome)) {
    # Infer the set of chromosomes from the tags
    tags <- getTags(this, collapse=NULL)
    chrTag <- grep("^chr", tags, value=TRUE)
    chrTag <- gsub("^chr", "", chrTag)
    chromosome <- as.integer(chrTag)
    # Sanity check
    .stop_if_not(is.finite(chromosome))
    this$.chromosome <- chromosome
  }

  chromosome
})

setMethodS3("getSampleName", "SegmentationDataFile", function(this, ...) {
  getName(this, ...)
})


setMethodS3("getReferenceName", "SegmentationDataFile", function(this, ..., force=FALSE) {
  referenceName <- this$.referenceName

  if (force || is.null(referenceName)) {
    # Infer the set of references from the tags
    tags <- getTags(this, collapse=NULL)
    idx <- grep("^chr", tags, value=FALSE)
    # Sanity check
    .stop_if_not(length(idx) == 1)
    tags <- tags[seq(from=idx+1, to=length(tags))]
    referenceName <- paste(tags, collapse=",")
    # Sanity check
    .stop_if_not(nchar(referenceName) > 0)
    this$.referenceName <- referenceName
  }

  referenceName
})

setMethodS3("loadFit", "SegmentationDataFile", abstract=TRUE)




setMethodS3("extractCopyNumberRegions", "SegmentationDataFile", function(this, ...) {
  fit <- loadFit(this, ...)
  res <- extractCopyNumberRegions(fit)
  res$sampleName <- getSampleName(this)
  res
}, protected=TRUE)