IRanges (version 2.6.0)

MaskCollection-class: MaskCollection objects

Description

The MaskCollection class is a container for storing a collection of masks that can be used to mask regions in a sequence.

Details

In the context of the Biostrings package, a mask is a set of regions in a sequence that need to be excluded from some computation. For example, when calling alphabetFrequency or matchPattern on a chromosome sequence, you might want to exclude some regions like the centromere or the repeat regions. This can be achieved by putting one or several masks on the sequence before calling alphabetFrequency on it.

A MaskCollection object is a vector-like object that represents such set of masks. Like standard R vectors, it has a "length" which is the number of masks contained in it. But unlike standard R vectors, it also has a "width" which determines the length of the sequences it can be "put on". For example, a MaskCollection object of width 20000 can only be put on an XString object of 20000 letters.

Each mask in a MaskCollection object x is just a finite set of integers that are >= 1 and <= width(x). When "put on" a sequence, these integers indicate the positions of the letters to mask. Internally, each mask is represented by a NormalIRanges object.

See Also

NormalIRanges-class, read.Mask, MaskedXString-class, reverse, alphabetFrequency, matchPattern

Examples

## Making a MaskCollection object:
  mask1 <- Mask(mask.width=29, start=c(11, 25, 28), width=c(5, 2, 2))
  mask2 <- Mask(mask.width=29, start=c(3, 10, 27), width=c(5, 8, 1))
  mask3 <- Mask(mask.width=29, start=c(7, 12), width=c(2, 4))
  mymasks <- append(append(mask1, mask2), mask3)
  mymasks
  length(mymasks)
  width(mymasks)
  collapse(mymasks)

  ## Names and descriptions:
  names(mymasks) <- c("A", "B", "C")  # names should be short and unique...
  mymasks
  mymasks[c("C", "A")]  # ...to make subsetting by names easier
  desc(mymasks) <- c("you can be", "more verbose", "here")
  mymasks[-2]

  ## Activate/deactivate masks:
  active(mymasks)["B"] <- FALSE
  mymasks
  collapse(mymasks)
  active(mymasks) <- FALSE  # deactivate all masks
  mymasks
  active(mymasks)[-1] <- TRUE  # reactivate all masks except mask 1
  active(mymasks) <- !active(mymasks)  # toggle all masks

  ## Other advanced operations:
  mymasks[[2]]
  length(mymasks[[2]])
  mymasks[[2]][-3]
  append(mymasks[-2], gaps(mymasks[2]))