match-utils: Utility functions operating on the matches returned by a...

In Bioconductor/Biostrings: Efficient manipulation of biological strings

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)
## S4 method for signature 'MIndex'
coverage(x, shift=0L, width=NULL, weight=1L)
## S4 method for signature 'MaskedXString'
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.

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.

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.

See Also

lowlevel-matching, matchPattern, matchPDict, XString-class, XStringViews-class, MIndex-class, coverage, align-utils in the pwalign package

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...

Bioconductor/Biostrings documentation built on Dec. 16, 2024, 8:46 a.m.