R/PairedPSCBS.extractSegmentDataByLocus.R

In PSCBS: Analysis of Parent-Specific DNA Copy Numbers

setMethodS3("extractSegmentDataByLocus", "PairedPSCBS", function(fit, fields=NULL, ..., verbose=FALSE) {
  # Extract data
  segs <- getSegments(fit, splitters=TRUE)
  data <- getLocusData(fit, ...)

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'fields':
  if (!is.null(fields)) {
    fields <- Arguments$getCharacters(fields)
    unknown <- fields[!is.element(fields, colnames(segs))]
    if (length(unknown) > 0L) {
      stop("Unknown segment fields: ", paste(sQuote(unknown), collapse=", "))
    }
  } else {
    fields <- colnames(segs)
  }

  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }


  verbose && enter(verbose, "Extracting segment data by locus")

  # Extract segment fields
  chromosome <- data$chromosome
  x <- data$x
  y <- data[,3L]
  segs <- segs[,fields]
  nbrOfLoci <- nrow(data)

  verbose && printf(verbose, "Segment fields: [%d] %s\n", length(fields), paste(sQuote(fields), collapse=", "))
  verbose && cat(verbose, "Number of loci: ", nbrOfLoci)

  # Allocate segment fields at the locus level
  dataL <- matrix(NA, nrow=nbrOfLoci, ncol=length(fields))
  colnames(dataL) <- fields
  dataL <- as.data.frame(dataL)

  verbose && cat(verbose, "Allocated results:")
  verbose && str(verbose, dataL)

  verbose && enter(verbose, "Extracting segment by segment")

  # For each segment...
  for (ss in seq_len(nrow(segs))) {
    verbose && enter(verbose, sprintf("Segment %d of %d", ss, nrow(segs)))
    seg <- segs[ss,]
    idxs <- which(chromosome == seg$chromosome &
                  seg$tcnStart <= x & x <= seg$tcnEnd)
    idxs <- Arguments$getIndices(idxs, max=nbrOfLoci)
    verbose && cat(verbose, "Number of loci in segment: ", length(idxs))
    # Sanity check
##    .stop_if_not(length(idxs) == seg$tcnNbrOfLoci)

    segsSS <- seg[fields]
    verbose && cat(verbose, "Segment data extracted:")
    verbose && print(verbose, segsSS)

    for (field in fields) {
      dataL[idxs,field] <- segsSS[[field]]
    }
    verbose && exit(verbose)
  } # for (ss ...)
  verbose && exit(verbose)

  # The calls for loci that have missing annotations or observations,
  # should also be missing, i.e. NA.
  nok <- (is.na(chromosome) | is.na(x) | is.na(y))
  dataL[nok,] <- NA

  # Sanity check
  .stop_if_not(nrow(dataL) == nbrOfLoci)
  .stop_if_not(ncol(dataL) == length(fields))

  verbose && exit(verbose)

  dataL
}, protected=TRUE) # extractSegmentDataByLocus()



##############################################################################
# HISTORY
# 2013-10-27
# o Added extractSegmentDataByLocus() for PairedPSCBS adopted from
#   extractCallsByLocus() of 'PSCBS'.
##############################################################################