matchLRPatterns {Biostrings}R Documentation

Find paired matches in a sequence

Description

The matchLRPatterns function finds paired matches in a sequence i.e. matches specified by a left pattern, a right pattern and a maximum distance between the left pattern and the right pattern.

Usage

  matchLRPatterns(Lpattern, Rpattern, max.ngaps, subject,
                  max.Lmismatch=0, max.Rmismatch=0,
                  with.Lindels=FALSE, with.Rindels=FALSE,
                  Lfixed=TRUE, Rfixed=TRUE)

Arguments

Lpattern The left part of the pattern.
Rpattern The right part of the pattern.
max.ngaps The max number of gaps in the middle i.e the max distance between the left and right parts of the pattern.
subject An XString, XStringViews or MaskedXString object containing the target sequence.
max.Lmismatch The maximum number of mismatching letters allowed in the left part of the pattern. If non-zero, an inexact matching algorithm is used (see the matchPattern function for more information).
max.Rmismatch Same as max.Lmismatch but for the right part of the pattern.
with.Lindels If TRUE then indels are allowed in the left part of the pattern. In that case max.Lmismatch is interpreted as the maximum "edit distance" allowed in the left part of the pattern.
See the with.indels argument of the matchPattern function for more information.
with.Rindels Same as with.Lindels but for the right part of the pattern.
Lfixed Only with a DNAString or RNAString subject can a Lfixed value other than the default (TRUE) be used.
With Lfixed=FALSE, ambiguities (i.e. letters from the IUPAC Extended Genetic Alphabet (see IUPAC_CODE_MAP) that are not from the base alphabet) in the left pattern _and_ in the subject are interpreted as wildcards i.e. they match any letter that they stand for.
See the fixed argument of the matchPattern function for more information.
Rfixed Same as Lfixed but for the right part of the pattern.

Value

An XStringViews object containing all the matches, even when they are overlapping (see the examples below), and where the matches are ordered from left to right (i.e. by ascending starting position).

Author(s)

H. Pages

See Also

matchPattern, matchProbePair, trimLRPatterns, findPalindromes, reverseComplement, XString-class, XStringViews-class, MaskedXString-class

Examples

  library(BSgenome.Dmelanogaster.UCSC.dm3)
  subject <- Dmelanogaster$chr3R
  Lpattern <- "AGCTCCGAG"
  Rpattern <- "TTGTTCACA"
  matchLRPatterns(Lpattern, Rpattern, 500, subject) # 1 match

  ## Note that matchLRPatterns() will return all matches, even when they are
  ## overlapping:
  subject <- DNAString("AAATTAACCCTT")
  matchLRPatterns("AA", "TT", 0, subject) # 1 match
  matchLRPatterns("AA", "TT", 1, subject) # 2 matches
  matchLRPatterns("AA", "TT", 3, subject) # 3 matches
  matchLRPatterns("AA", "TT", 7, subject) # 4 matches

[Package Biostrings version 2.12.9 Index]