R/SnpChipEffectSet.extractAlleleSet.R

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

setMethodS3("extractAlleleSet", "SnpChipEffectSet", function(this, units=NULL, sortUnits=TRUE, transform=log2, ..., verbose=FALSE) {
  requireNamespace("oligoClasses") || throw("Package not loaded: oligoClasses")


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Sanity check
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  chipType <- getChipType(this, fullname=FALSE)

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  cdf <- getCdf(this)

  # Argument 'units':
  if (is.null(units)) {
    # Identify all SNP_A-* units (as what is returned by oligo)
    units <- indexOf(cdf, pattern="^SNP_A-")
  } else {
    units <- Arguments$getIndices(units, max=nbrOfUnits(cdf))
  }

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


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Order units lexicographically by their names?
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  unitNames <- getUnitNames(cdf, units=units)
  if (sortUnits) {
    verbose && enter(verbose, "Sort units by their names")
    srt <- sort(unitNames, method="quick", index.return=TRUE)
    unitNames <- srt$x
    units <- units[srt$ix]
    # Not needed anymore
    srt <- NULL;  # Not needed anymore
    verbose && exit(verbose)
  }


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Inferring what unit groups to extract
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  verbose && enter(verbose, "Inferring the number of groups to extract")
  verbose && cat(verbose, "Chip type: ", getChipType(this))
  ugcMap <- getUnitGroupCellMap(this, units=units, verbose=verbose)
  maxGroup <- max(ugcMap$group, na.rm=TRUE)
  # Not needed anymore
  ugcMap <- NULL
  verbose && cat(verbose, "Max number of groups unit (unit,group,cell) map: ", maxGroup)
  if (maxGroup > 4) {
    maxGroup <- 4L
  }

  # Sanity check
  if (!is.element(maxGroup, c(2,4))) {
    throw("Unsupported value on 'maxGroup': ", maxGroup)
  }

  groups <- 1:maxGroup

  verbose && cat(verbose, "Groups to extract: ", seqToHumanReadable(groups))
  verbose && exit(verbose)


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Infer which (antisense, sense) unit groups to swap (more below)
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  if (maxGroup == 4) {
    verbose && enter(verbose, "Inferring which unit groups to be swapped to (sense, antisense)")

    # Make sure pairs are order as (sense, antisense)
    dirs <- getGroupDirections(cdf, units=units, verbose=less(verbose, 5))
    names(dirs) <- NULL

    gc <- gc()
    verbose && print(verbose, gc)

    # Sanity check
    lens <- sapply(dirs, FUN=length)
    uLens <- unique(lens)
    if (any(!is.element(uLens, unique(c(2,maxGroup))))) {
      throw("Internal error: Unexpected number of unit groups: ",
                                                paste(uLens, collapse=", "))
    }

    # Extract the direction/strand of the first group
    # dirs <- lapply(dirs, FUN=function(groups) groups[1])
    dirs <- lapply(dirs, FUN=.subset, 1L)
    dirs <- unlist(dirs, use.names=FALSE)

    # Identify which to swap from (antisense,sense) to (sense,antisense)
    idxs <- which(dirs == 2)
    # Not needed anymore
    dirs <- NULL

    gc <- gc()
    verbose && print(verbose, gc)

    verbose && exit(verbose)
  }

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Extract data
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  verbose && enter(verbose, "Extracting data")
  theta <- extractTheta(this, groups=groups, units=units, verbose=verbose)

  # Not needed anymore
  # Not needed anymore
  units <- NULL

  gc <- gc()
  verbose && print(verbose, gc)

  verbose && exit(verbose)


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Swap (antisense, sense) unit groups to (sense, antisense)
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  if (maxGroup == 4 && length(idxs) > 0) {
    verbose && enter(verbose, "Ordering unit groups to be (sense, antisense)")
    verbose && cat(verbose, "Swapping elements:")
    verbose && str(verbose, idxs)
    theta[idxs,,] <- theta[idxs,c(3,4,1,2),,drop=FALSE]
    # Not needed anymore
    idxs <- NULL;   # Not needed anymore
    gc <- gc()
    verbose && print(verbose, gc)
    verbose && exit(verbose)
  }


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Transform data
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  if (!is.null(transform)) {
    verbose && enter(verbose, "Transforming signals")
    theta <- transform(theta)
    verbose && str(verbose, theta)
    gc <- gc()
    verbose && print(verbose, gc)
    verbose && exit(verbose)
  }


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Allocate and populate AlleleSet
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  verbose && enter(verbose, "Allocate and populate AlleleSet")
  if (maxGroup == 2) {
    res <- new("AlleleSet",
      alleleA = theta[,1,,drop=TRUE],
      alleleB = theta[,2,,drop=TRUE]
    )
  } else if (maxGroup == 4) {
    res <- new("AlleleSet",
      antisenseAlleleA = theta[,3,,drop=TRUE],
      senseAlleleA     = theta[,1,,drop=TRUE],
      antisenseAlleleB = theta[,4,,drop=TRUE],
      senseAlleleB     = theta[,2,,drop=TRUE]
    )
  }

  # Not needed anymore
  # Not needed anymore
  theta <- NULL

  # Assign feature data
  .featureNames(res) <- unitNames
  # Not needed anymore
  unitNames <- NULL

  # Assign annotation data
  pdPkgName <- .cleanPlatformName(chipType)
  .annotation(res) <- pdPkgName

  # Assign sample names
  filenames <- sapply(this, getFilename)
  names(filenames) <- NULL
  filenames <- gsub(",chipEffects", "", filenames)
  .sampleNames(res) <- filenames

  verbose && exit(verbose)

  res
})