R/CopyNumberOutliers.R

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

setConstructorS3("CopyNumberOutliers", function(start=NULL, stop=NULL, mean=NULL, count=NULL, call=NULL, ...) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  extend(Object(), "CopyNumberOutliers",
    start = start,
    stop = stop,
    mean = mean,
    count = count,
    call= call,
    ...
  )
})


setMethodS3("as.character", "CopyNumberOutliers", function(x, ...) {
  # To please R CMD check
  this <- x

  s <- sprintf("%s:", class(this)[1])
  s <- c(s, sprintf("Number of regions: %d", nbrOfRegions(this)))

  GenericSummary(s)
}, protected=TRUE)


setMethodS3("nbrOfRegions", "CopyNumberOutliers", function(this, ...) {
  length(this$start)
})


setMethodS3("as.data.frame", "CopyNumberOutliers", function(x, ...) {
  # To please R CMD check
  this <- x

  data <- cbind(start=this$start, stop=this$stop, mean=this$mean, count=this$count, call=this$call)
  data
})


setMethodS3("applyRegions", "CopyNumberOutliers", function(this, FUN, ...) {
  data <- as.data.frame(this)
  o <- order(data[,"start"])
  data <- data[o,,drop=FALSE]
  apply(data, MARGIN=1, FUN=FUN)
}, protected=TRUE)


setMethodS3("drawLevels", "CopyNumberOutliers", function(this, col="red", lwd=2, lty=1, xScale=1e-6, yScale=1, ...) {
  col0 <- col
  lwd0 <- lwd
  lty0 <- lty
  applyRegions(this, FUN=function(cnr) {
    x <- c(cnr["start"], cnr["stop"])
    y <- rep(cnr["mean"], times=2)
    if (is.function(col0))
      col <- col0(cnr)
    if (is.function(lwd0))
      lwd <- lwd0(cnr)
    if (is.function(lty0))
      lty <- lty0(cnr)
    lines(x=xScale*x, y=yScale*y, col=col, lwd=lwd, lty=lty, ...)
  })
})



setMethodS3("lines", "CopyNumberOutliers", function(x, col="red", lwd=2, xScale=1e-6, yScale=1, ...) {
  # To please R CMD check.
  this <- x

  data <- as.data.frame(this)
  o <- order(data[,"start"])
  data <- data[o,,drop=FALSE]
  xx <- t(data[,c("start", "stop"),drop=FALSE])
  yy <- rep(this$mean[o], each=2)
  lines(x=xScale*xx, y=yScale*yy, col=col, lwd=lwd, ...)
})