matchLRPatterns: Find paired matches in a sequence
In Biostrings: Efficient manipulation of biological strings

Description Usage Arguments Value Author(s) See Also Examples

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.

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

`Lpattern`	The left part of the pattern.
`Rpattern`	The right part of the pattern.
`max.gaplength`	The max length of the gap 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. `Lfixed` can also be a character vector, a subset of `c("pattern", "subject")`. `Lfixed=c("pattern", "subject")` is equivalent to `Lfixed=TRUE` (the default). An empty vector is equivalent to `Lfixed=FALSE`. With `Lfixed="subject"`, ambiguities in the pattern only are interpreted as wildcards. With `Lfixed="pattern"`, ambiguities in the subject only are interpreted as wildcards.
`Rfixed`	Same as `Lfixed` but for the right part of the pattern.

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).

H. Pag<c3><a8>s

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

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