R/ChromosomalModel.getXTheta.R

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

setMethodS3("getPcuTheta", "ChromosomalModel", function(this, chromosome, reorder=TRUE, ..., force=FALSE, verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }


  verbose && enter(verbose, "Extracting (position, theta+)")

  # Get (position, chipType, unit) map
  pcu <- getPositionChipTypeUnit(this, chromosome=chromosome, 
                                                  verbose=less(verbose, 20))

  # Get list of chip-effect sets
  cesList <- getSets(this)

  # Allocate return structure
  naValue <- NA_real_
  theta <- matrix(naValue, nrow=nrow(pcu), ncol=length(this))

  for (kk in seq_along(cesList)) {
    verbose && enter(verbose, "Chip type #", kk, " of ", length(cesList))
    ces <- cesList[[kk]]
    idxs <- which(as.integer(pcu[,"chipType"]) == kk)
    units <- pcu[idxs,"unit"]
    verbose && cat(verbose, "Units: ")
    verbose && str(verbose, units)

    verbose && enter(verbose, "Reading data across chip-effect files")
    theta[idxs,] <- extractMatrix(ces, units=units, verbose=less(verbose, 20))
    verbose && exit(verbose)

    verbose && exit(verbose)
  }

  verbose && exit(verbose)

  list(pcu=pcu, theta=theta)
}, protected=TRUE);  # getPcuTheta()