R/AbstractCNData.R

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

###########################################################################/**
# @RdocClass AbstractCNData
#
# @title "The AbstractCNData class"
#
# \description{
#  @classhierarchy
#
#  An AbstractCNData object holds copy number data.
# }
#
# @synopsis
#
# \arguments{
#   \item{chromosome}{(Optional) An @integer scalar (or a @vector of length J),
#        which can be used to specify which chromosome each locus belongs to
#        in case multiple chromosomes are segments.
#        This argument is also used for annotation purposes.}
#   \item{x}{Optional @numeric @vector of J genomic locations.
#            If @NULL, index locations \code{1:J} are used.}
#   \item{y}{Optional @numeric @vector of J genomic locations.}
#   \item{...}{Optional named locus-specific signal @vectors of length J.}
#   \item{name}{Optional @character string.}
#   \item{.virtuals}{(Internal) a @list with virtual column name @functions.}
# }
#
# \section{Fields and Methods}{
#  @allmethods "public"
# }
#
# @author
#*/###########################################################################
setConstructorS3("AbstractCNData", function(chromosome=NULL, x=NULL, y=NULL, ..., name=NULL, .virtuals=NULL) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  if (!is.null(chromosome)) {
    # Argument 'chromosome':
    if (is.data.frame(chromosome)) {
      data <- chromosome
      chromosome <- data$chromosome
      x <- data$x
      y <- data$y
    }

    # Any extra locus signals?
    args <- list(...)
    keep <- !sapply(args, FUN=is.null)
    args <- args[keep]

    if (is.null(y)) {
      y <- args$y
      args$y <- NULL
    }
  } else {
    args <- NULL
  }

# str(list(chromosome=chromosome, x=x, cn=cn))


##  cat("AbstractCNData...\n")

  this <- extend(RawGenomicSignals(chromosome=chromosome, x=x, y=y, name=name), "AbstractCNData")

  this <- setVirtualColumnFunctions(this, .virtuals)

## print(class(this))

  if (length(args) > 0) {
    class <- class(this)
    for (key in names(args)) {
      values <- args[[key]]
      this[[key]] <- values
    }
    class(this) <- class
  }
##print(class(this))


##print(head(as.data.frame(this)))
##  cat("AbstractCNData...done\n")

  this
})


setMethodS3("getPlatform", "AbstractCNData", function(this, ...) {
  attr(this, "platform")
})



setMethodS3("setPlatform", "AbstractCNData", function(this, platform, ...) {
  platform <- Arguments$getCharacter(platform)
  attr(this, "platform") <- platform
  invisible(this)
})


setMethodS3("getChipType", "AbstractCNData", function(this, fullname=TRUE, ...) {
  chipType <- attr(this, "chipType")
  if (!fullname) {
    chipType <- gsub(",.*", "", chipType)
  }
  chipType
})

setMethodS3("setChipType", "AbstractCNData", function(this, chipType, ...) {
  chipType <- Arguments$getCharacter(chipType)
  attr(this, "chipType") <- chipType
  invisible(this)
})


setMethodS3("getLocusData", "AbstractCNData", function(this, ...) {
  as.data.frame(this)
})



setMethodS3("hasKnownPositions", "AbstractCNData", function(this, ...) {
  data <- as.data.frame(this, ...)
  ok <- (!is.na(data$chromosome) & !is.na(data$x))
  ok
}, protected=TRUE)



setMethodS3("orderAlongGenome", "AbstractCNData", function(this, ...) {
  sort(this, ...)
}, protected=TRUE)



setMethodS3("findLargeGaps", "AbstractCNData", function(chromosome, ...) {
  pkg <- "PSCBS"
  require(pkg, character.only=TRUE) || throw("Package not loaded: ", pkg)

  # To please R CMD check
  this <- chromosome

  data <- as.data.frame(this, ...)
  findLargeGaps(chromosome=data$chromosome, x=data$x, ...)
}) # findLargeGaps()