MaskCollection-class {Biostrings} | R Documentation

## 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.

### Basic accesor methods

In the code snippets below, `x` is a MaskCollection object.

  `length(x)`: The number of masks in `x`.
  `width(x)`: The common with of all the masks in `x`. This determines the length of the sequences that `x` can be "put on".
  `active(x)`: A logical vector of the same length as `x` where each element indicates whether the corresponding mask is active or not.
  `names(x)`: `NULL` or a character vector of the same length as `x`.
  `nir_list(x)`: A list of the same length as `x`, where each element is a NormalIRanges object representing a mask in `x`.

### Constructor

  `Mask(mask.width, start=NULL, end=NULL, width=NULL)`: Return a single mask (i.e. a MaskCollection object of length 1) of width `mask.width` (a single integer >= 1) and masking the ranges of positions specified by `start`, `end` and `width`. See the `IRanges` constructor (`?IRanges`) for how `start`, `end` and `width` can be specified. Note that the returned mask is active and unnamed.

### Other methods

In the code snippets below, `x` is a MaskCollection object.

  `isEmpty(x)`: Return a logical vector of the same length as `x`, indicating, for each mask in `x`, whether it's empty or not.
  `max(x)`: The greatest (or last, or rightmost) masked position for each mask. This is a numeric vector of the same length as `x`.
  `min(x)`: The smallest (or first, or leftmost) masked position for each mask. This is a numeric vector of the same length as `x`.
  `maskedwidth(x)`: The number of masked position for each mask. This is an integer vector of the same length as `x` where all values are >= 0 and <= `width(x)`.
  `maskedratio(x)`: `maskedwidth(x) / width(x)`

### Subsetting and appending

In the code snippets below, `x` is a MaskCollection object.

  `x[i]`: Return a new MaskCollection object made of the selected masks. `i` can be a numeric vector, a logical vector, `NULL` or missing.
  `append(x, values, after=length(x))`: Add masks to `x`.
  `x[[i]]`: Extract the i-th mask as a NormalIRanges object.

### Other methods

In the code snippets below, `x` is a MaskCollection object.

  `narrow(x, start=NA, end=NA, width=NA, use.names=TRUE)`: Narrow the masks in `x`.
  `reduce(x)`: Return a MaskCollection object of length 1 made of the union (or merging, or collapsing) of all the active masks in `x`.
  `gaps(x)`: Invert the masks in `x`.

### Author(s)

H. Pages

### See Also

MaskedXString-class, `maskMotif`, `alphabetFrequency`, `reverse`, `matchPattern`, NormalIRanges-class

### 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)
      reduce(mymasks)
      gaps(mymasks)

      ## Putting a MaskCollection object on a sequence:
      x <- DNAString("ACACAACTAGATAGNACTNNGAGAGACGC")
      x
      length(x)  # same as width(mymasks)
      nchar(x)   # same as length(x)
      masks(x) <- mymasks
      x
      length(x)  # has not changed
      nchar(x)   # has changed
      alphabetFrequency(x)

      ## Removing the masks:
      masks(x) <- NULL
      x
      alphabetFrequency(x)

      ## Active/inactive masks:
      reduce(mymasks)
      active(mymasks)[2] <- FALSE
      mymasks
      reduce(mymasks)

      ## Other advanced operations:
      mymasks[[2]]
      length(mymasks[[2]])
      mymasks[[2]][-3]
      append(mymasks[-2], gaps(mymasks[2]))
      mymasks2 <- narrow(mymasks, start=8)
      mymasks2
      mymasks2[[2]]

[Package Biostrings version 2.8.18 Index]