R/CopyNumberRegions.EXT2.R

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

setMethodS3("getChromosomes", "CopyNumberRegions", function(this, ...) {
  sort(unique(this$chromosome))
})


setMethodS3("nbrOfChromosomes", "CopyNumberRegions", function(this, ...) {
  length(getChromosomes(this))
})


setMethodS3("unique", "CopyNumberRegions", function(x, ...) {
  # To please R CMD check
  this <- x

  # Keep only unique regions
  data <- as.data.frame(this)
  data <- unique(data)
  fields <- colnames(data)
  res <- clone(this)
  for (field in fields) {
    res[[field]] <- data[[field]]
  }

  res
})

setMethodS3("append", "CopyNumberRegions", function(this, other, ...) {
  # Argument 'other':
  other <- Arguments$getInstanceOf(other, class(this)[1])

  data <- as.data.frame(this)
  fields <- colnames(data)
  for (field in fields) {
    values <- c(this[[field]], other[[field]])
    this[[field]] <- values
  }

  invisible(this)
})