Biostrings (version 2.40.2)

match-utils: Utility functions operating on the matches returned by a high-level matching function

Description

Miscellaneous utility functions operating on the matches returned by a high-level matching function like matchPattern, matchPDict, etc...

Usage

mismatch(pattern, x, fixed=TRUE)
nmatch(pattern, x, fixed=TRUE)
nmismatch(pattern, x, fixed=TRUE)
"coverage"(x, shift=0L, width=NULL, weight=1L)
"coverage"(x, shift=0L, width=NULL, weight=1L)

Arguments

pattern

The pattern string.

x

An XStringViews object for mismatch (typically, one returned by matchPattern(pattern, subject)).

An MIndex object for coverage, or any object for which a coverage method is defined. See ?coverage.

fixed

See ?`lowlevel-matching`.

shift, width

See ?coverage.

weight

An integer vector specifying how much each element in x counts.

Value

mismatch: a list of integer vectors.nmismatch: an integer vector containing the length of the vectors produced by mismatch.coverage: an Rle object indicating the coverage of x. See ?coverage for the details. If x is an MIndex object, the coverage of a given position in the underlying sequence (typically the subject used during the search that returned x) is the number of matches (or hits) it belongs to.

Details

The mismatch function gives the positions of the mismatching letters of a given pattern relatively to its matches in a given subject.

The nmatch and nmismatch functions give the number of matching and mismatching letters produced by the mismatch function.

The coverage function computes the "coverage" of a subject by a given pattern or set of patterns.

See Also

lowlevel-matching, matchPattern, matchPDict, XString-class, XStringViews-class, MIndex-class, coverage, align-utils

Examples

  ## ---------------------------------------------------------------------
  ## mismatch() / nmismatch()
  ## ---------------------------------------------------------------------
  subject <- DNAString("ACGTGCA")
  m <- matchPattern("NCA", subject, max.mismatch=1, fixed=FALSE)
  mismatch("NCA", m)
  nmismatch("NCA", m)

  ## ---------------------------------------------------------------------
  ## coverage()
  ## ---------------------------------------------------------------------
  coverage(m)

  ## See ?matchPDict for examples of using coverage() on an MIndex object...