R/CopyNumberOutliers.FOREIGN.R

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

setMethodS3("extractCopyNumberOutliers", "profileCGH", function(object, ...) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  pv <- object$profileValues

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Allocate result table
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Identify unique regions
  uRegions <- unique(pv$Region)
  nbrOfRegions <- length(uRegions)

  # Columns
  colClasses <- c(chromosome="character", start="integer", 
                  stop="integer", mean="double", nbrOfLoci="integer",
                  call="character")
  df <- dataFrame(colClasses, nrow=nbrOfRegions)


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Extract each region
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  for (rr in seq_along(uRegions)) {
    # Get the region ID
    region <- uRegions[rr]

    # Get the first and last position of each region
    idx <- which(region == pv$Region)
    idx <- idx[c(1,length(idx))]
    idx1 <- idx[1]

    # Chromosome
    df[rr,"chromosome"] <- pv$Chromosome[idx1]

    # (start, stop, length)
    df[rr,c("start", "stop")] <- as.integer(pv$PosBase[idx])

    # Number of SNPs
    df[rr,"nbrOfLoci"] <- as.integer(diff(idx)+1)

    # Smoothing
    df[rr,"mean"] <- pv$Smoothing[idx1]

    # Call
    df[rr,"call"] <- c("loss", "neutral", "gain")[pv$ZoneGNL[idx1]+2]
  }


  CopyNumberOutliers(
    start=df$start, 
    stop=df$stop, 
    mean=df$mean, 
    count=df$nbrOfLoci,
    call=df$call
  )
})


setMethodS3("extractCopyNumberOutliers", "DNAcopy", function(object, ...) {
  output <- object$output

  CopyNumberOutliers(
    start=output[["loc.start"]], 
    stop=output[["loc.end"]], 
    mean=output[["seg.mean"]],
    count=output[["num.mark"]]
  )
})