gregexpr2 {Biostrings} | R Documentation

## A replacement for R standard gregexpr function

### Description

This is a replacement for the standard gregexpr function that does exact matching only. Standard gregexpr() misses matches when they are overlapping. The gregexpr2 function finds all matches but it only works in "fixed" mode i.e. for exact matching (regular expressions are not supported).

### Usage

    gregexpr2(pattern, text)

### Arguments

`pattern` | character string to be matched in the given character vector
`text` | a character vector where matches are sought

### Value

A list of the same length as `text` each element of which is an integer vector as in `gregexpr`, except that the starting positions of all (even overlapping) matches are given. Note that, unlike `gregexpr`, `gregexpr2` doesn't attach a "match.length" attribute to each element of the returned list because, since it only works in "fixed" mode, then all the matches have the length of the pattern. Another difference with `gregexpr` is that with `gregexpr2`, the `pattern` argument must be a single (non-NA, non-empty) string.

### Author(s)

H. Pagès

### See Also

`gregexpr`, `matchPattern`

### Examples

        gregexpr("aa", c("XaaaYaa", "a"), fixed=TRUE)
        gregexpr2("aa", c("XaaaYaa", "a"))

[Package Biostrings version 2.52.0 Index]