maskMotif {Biostrings} | R Documentation

## Masking by content (or by position)

### Description

Functions for masking a sequence by content (or by position).

### Usage

    maskMotif(x, motif, min.block.width=1, ...)
    mask(x, start=NA, end=NA, pattern)

### Arguments

`x` | The sequence to mask.
`motif` | The motif to mask in the sequence.
`min.block.width` | The minimum width of the blocks to mask.
`...` | Additional arguments for `matchPattern`.
`start` | An integer vector containing the starting positions of the regions to mask.
`end` | An integer vector containing the ending positions of the regions to mask.
`pattern` | The motif to mask in the sequence.

### Value

A MaskedXString object for `maskMotif` and an XStringViews object for `mask`.

### Author(s)

H. Pagès

### See Also

`read.Mask`, `matchPattern`, XString-class, MaskedXString-class, XStringViews-class, MaskCollection-class

### Examples

      ## ---------------------------------------------------------------------
      ## EXAMPLE 1
      ## ---------------------------------------------------------------------

      maskMotif(BString("AbcbbcbEEE"), "bcb")
      maskMotif(BString("AbcbcbEEE"), "bcb")

      ## maskMotif() can be used in an incremental way to mask more than 1
      ## motif. Note that maskMotif() does not try to mask again what's
      ## already masked (i.e. the new mask will never overlaps with the
      ## previous masks) so the order in which the motifs are masked actually
      ## matters as it will affect the total set of masked positions.
      x0 <- BString("AbcbEEEEEbcbbEEEcbbcbc")
      x1 <- maskMotif(x0, "E")
      x1
      x2 <- maskMotif(x1, "bcb")
      x2
      x3 <- maskMotif(x2, "b")
      x3
      ## Note that inverting the order in which "b" and "bcb" are masked would
      ## lead to a different final set of masked positions.
      ## Also note that the order doesn't matter if the motifs to mask don't
      ## overlap (we assume that the motifs are unique) i.e. if the prefix of
      ## each motif is not the suffix of any other motif. This is of course
      ## the case when all the motifs have only 1 letter.

      ## ---------------------------------------------------------------------
      ## EXAMPLE 2
      ## ---------------------------------------------------------------------

      x <- DNAString("ACACAACTAGATAGNACTNNGAGAGACGC")

      ## Mask the N-blocks
      x1 <- maskMotif(x, "N")
      x1
      as(x1, "Views")
      gaps(x1)
      as(gaps(x1), "Views")

      ## Mask the AC-blocks
      x2 <- maskMotif(x1, "AC")
      x2
      gaps(x2)

      ## Mask the GA-blocks
      x3 <- maskMotif(x2, "GA", min.block.width=5)
      x3  # masks 2 and 3 overlap
      gaps(x3)

      ## ---------------------------------------------------------------------
      ## EXAMPLE 3
      ## ---------------------------------------------------------------------

      library(BSgenome.Dmelanogaster.UCSC.dm3)
      chrU <- Dmelanogaster$chrU
      chrU
      alphabetFrequency(chrU)
      chrU <- maskMotif(chrU, "N")
      chrU
      alphabetFrequency(chrU)
      as(chrU, "Views")
      as(gaps(chrU), "Views")

      mask2 <- Mask(mask.width=length(chrU),
                    start=c(50000, 350000, 543900), width=25000)
      names(mask2) <- "some ugly regions"
      masks(chrU) <- append(masks(chrU), mask2)
      chrU
      as(chrU, "Views")
      as(gaps(chrU), "Views")

      ## ---------------------------------------------------------------------
      ## EXAMPLE 4
      ## ---------------------------------------------------------------------
      ## Note that unlike maskMotif(), mask() returns an XStringViews object!

      ## masking "by position"
      mask("AxyxyxBC", 2, 6)

      ## masking "by content"
      mask("AxyxyxBC", "xyx")
      noN_chrU <- mask(chrU, "N")
      noN_chrU
      alphabetFrequency(noN_chrU, collapse=TRUE)

[Package Biostrings version 2.60.2 Index]