match-utils            package:Biostrings            R Documentation

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

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...

