read.agpMask(file, seqname="?", mask.width=NA, gap.types=NULL, use.gap.types=FALSE)
read.gapMask(file, seqname="?", mask.width=NA, gap.types=NULL, use.gap.types=FALSE)
read.liftMask(file, seqname="?", mask.width=NA)
read.rmMask(file, seqname="?", mask.width=NA, use.IDs=FALSE)
read.trfMask(file, seqname="?", mask.width=NA)

## ---------------------------------------------------------------------
  ## A. Extract a mask of assembly gaps ("AGAPS" mask) with read.agpMask()
  ## ---------------------------------------------------------------------
  ## Note: The hs_b36v3_chrY.agp file was obtained by downloading,
  ## extracting and renaming the hs_ref_chrY.agp.gz file from
  ##
  ##   ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/Assembled_chromosomes/
  ##     hs_ref_chrY.agp.gz      5 KB  24/03/08  04:33:00 PM
  ##
  ## on May 9, 2008.

  chrY_length <- 57772954
  file1 <- system.file("extdata", "hs_b36v3_chrY.agp", package="IRanges")
  mask1 <- read.agpMask(file1, seqname="chrY", mask.width=chrY_length,
                        use.gap.types=TRUE)
  mask1
  mask1[[1]]

  mask11 <- read.agpMask(file1, seqname="chrY", mask.width=chrY_length,
                         gap.types=c("centromere", "heterochromatin"))
  mask11[[1]]

  ## ---------------------------------------------------------------------
  ## B. Extract a mask of assembly gaps ("AGAPS" mask) with read.liftMask()
  ## ---------------------------------------------------------------------
  ## Note: The hg18liftAll.lft file was obtained by downloading,
  ## extracting and renaming the liftAll.zip file from
  ##
  ##   http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/
  ##     liftAll.zip             03-Feb-2006 11:35  5.5K
  ##
  ## on May 8, 2008.

  file2 <- system.file("extdata", "hg18liftAll.lft", package="IRanges")
  mask2 <- read.liftMask(file2, seqname="chr1")
  mask2
  if (interactive()) {
      ## contigs 7 and 8 for chrY are adjacent
      read.liftMask(file2, seqname="chrY")

      ## displays the sequence names found in the file
      read.liftMask(file2)

      ## specify an unknown sequence name
      read.liftMask(file2, seqname="chrZ", mask.width=300)
  }

  ## ---------------------------------------------------------------------
  ## C. Extract a RepeatMasker ("RM") or Tandem Repeats Finder ("TRF")
  ##    mask with read.rmMask() or read.trfMask()
  ## ---------------------------------------------------------------------
  ## Note: The ce2chrM.fa.out and ce2chrM.bed files were obtained by
  ## downloading, extracting and renaming the chromOut.zip and
  ## chromTrf.zip files from
  ##
  ##   http://hgdownload.cse.ucsc.edu/goldenPath/ce2/bigZips/
  ##     chromOut.zip            21-Apr-2004 09:05  2.6M
  ##     chromTrf.zip            21-Apr-2004 09:07  182K
  ##
  ## on May 7, 2008.

  ## Before you can extract a mask with read.rmMask() or read.trfMask(), you
  ## need to know the length of the sequence that you're going to put the
  ## mask on:
  if (interactive()) {
      library(BSgenome.Celegans.UCSC.ce2)
      chrM_length <- seqlengths(Celegans)[["chrM"]]

      ## Read the RepeatMasker .out file for chrM in ce2:
      file3 <- system.file("extdata", "ce2chrM.fa.out", package="IRanges")
      RMmask <- read.rmMask(file3, seqname="chrM", mask.width=chrM_length)
      RMmask

      ## Read the Tandem Repeats Finder .bed file for chrM in ce2:
      file4 <- system.file("extdata", "ce2chrM.bed", package="IRanges")
      TRFmask <- read.trfMask(file4, seqname="chrM", mask.width=chrM_length)
      TRFmask
      desc(TRFmask) <- paste(desc(TRFmask), "[period<=12]")
      TRFmask

      ## Put the 2 masks on chrM:
      chrM <- Celegans$chrM
      masks(chrM) <- RMmask  # this would drop all current masks, if any
      masks(chrM) <- append(masks(chrM), TRFmask)
      chrM
  }