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.
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. Pages

See Also

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

Examples

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

  maskMotif(BString("AbcbcbDE"), "bcb")

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

  x <- DNAString("ACACAACTAGATAGNACTNNGAGAGACGC")

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

  ## 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, "XStringViews")
  as(gaps(chrU), "XStringViews")

  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, "XStringViews")
  as(gaps(chrU), "XStringViews")

  ## ---------------------------------------------------------------------
  ## 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 2.8.18 Index]