R/dropCellsFromCdfList.R

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

# @author "HB"
dropCellsFromCdfList <- function(cdfList, maxNbrOfCells, cellsToExclude, ..., verbose=0) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'cdfList':
  if (!is.list(cdfList)) {
    stop("Argument 'cdfList' is not a list: ", mode(cdfList))
  }

  # Argument 'maxNbrOfCells':
  maxNbrOfCells <- as.integer(maxNbrOfCells)
  if (maxNbrOfCells < 1) {
    stop("Argument 'maxNbrOfCells' is non-positive: ", maxNbrOfCells)
  }

  # Argument 'cellsToExclude':
  cellsToExclude <- as.integer(cellsToExclude)
  if (any(cellsToExclude < 1 | cellsToExclude > maxNbrOfCells)) {
    stop(sprintf("Argument 'cellsToExclude' is out of range [1,%d].", maxNbrOfCells))
  }


  nbrOfUnits <- length(cdfList)

  if(verbose >= 1) {
    cat("Excluding cells from CDF list structure...\n")
    cat("Number of units: ", nbrOfUnits, "\n", sep="")
    cat("Number of cells to exclude: ", length(cellsToExclude), "\n", sep="")
  }

  toExclude <- logical(maxNbrOfCells)
  toExclude[cellsToExclude] <- TRUE

  # Sanity check (cannot drop all cells)
  stopifnot(!all(toExclude))

  # Nothing todo?
  if (!any(toExclude)) {
    if(verbose >= 1) {
      cat("No cells to be exclude. Skipping.\n")
      cat("Excluding cells from CDF list structure...done\n")
    }
    return(cdfList)
  }

  if(verbose >= 1) {
    cat("Number of units left: ")
  }

  # Number of cells dropped from CDF
  nDrop <- 0L

  # Total number of cells
  nCells <- 0L

  fields <- c("x", "y", "indices", "pbase", "tbase", "atom", "indexpos")
  for (jj in seq_len(nbrOfUnits)) {
    if(verbose >= 1 && jj %% 10e3 == 1) {
      cat(nbrOfUnits-jj+1L, ", ", sep="")
    }

    cdfUnit <- cdfList[[jj]]

    # Total number of cells in unit
    nbrOfAtoms <- 0L
    nbrOfCells <- 0L

    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # Update the groups
    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    groups <- cdfUnit[["groups"]]

    # Number of cells dropped for this unit
    nDropUU <- 0L
    nCellsUU <- 0L

    nbrOfGroups <- length(groups)
    for (gg in seq_len(nbrOfGroups)) {
      group <- groups[[gg]]

      indices <- group$indices
      nCellsGG <- length(indices)
      nCellsUU <- nCellsUU + nCellsGG
      toExcludeGG <- toExclude[indices]
      drop <- which(toExcludeGG)
##print(list(indices=indices, drop=drop, toExcludeGG=toExcludeGG))
      nDropGG <- length(drop)

      # Sanity check (assuming not all cells are dropped)
      ## stopifnot(nDropGG < nCellsGG)

      nbrOfCellsGG <- nCellsGG - nDropGG


      if (nDropGG > 0) {
        keep <- which(!toExcludeGG)
##print(list(unit=jj, group=gg, keep=keep))
        for (field in fields) {
          value <- group[[field]]
          value <- value[keep]
          group[[field]] <- value
        }

        # The 'atom' and 'indexpos' fields must be "complete" (I think)
        group$atom <- seq_len(nbrOfCellsGG)
        group$indexpos <- seq_len(nbrOfCellsGG)
#print(group)

        nDropUU <- nDropUU + nDropGG
      }

      # Hmm... (is the following true)
      nbrOfAtomsGG <- nbrOfCellsGG

      # Update the group count
      group$natoms <- nbrOfAtomsGG
      group$ncells <- nbrOfCellsGG

      nbrOfAtoms <- nbrOfAtoms + nbrOfAtomsGG
      nbrOfCells <- nbrOfCells + nbrOfCellsGG

      groups[[gg]] <- group
    } # for (gg ...)

    cdfUnit[["groups"]] <- groups

    nDrop <- nDrop + nDropUU
    nCells <- nCells + nCellsUU

    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # Update the unit counts
    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # Total number of cells in unit
    cdfUnit$natoms <- nbrOfAtoms
    cdfUnit$ncells <- nbrOfCells

    cdfList[[jj]] <- cdfUnit
  } # for (jj ...)

  if(verbose >= 1) {
    cat("0.\n")
    cat("Total number of cells: ", nCells, "\n")
    cat("Number of cells dropped: ", nDrop, "\n")
    cat("Excluding cells from CDF list structure...done\n")
  }

  cdfList
} # dropCellsFromCdfList()