matchLRPatterns {Biostrings} | R Documentation

## Find patterns defined by a left and a right part in a sequence

### Description

[TODO]

### Usage

      matchLRPatterns(Lpattern, Rpattern, max.ngaps, subject,
                      max.Lmismatch=0, max.Rmismatch=0,
                      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.
`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`, `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 2.8.18 Index]