regexCounts {sarks}R Documentation

Count occurrences of regular expression

Description

Counts how often a regular expression (or vector of regular expressions) occurs in each element of a character vector.

Usage

regexCounts(regex, seqs, overlap = FALSE)

Arguments

regex

character vector of regular expressions to search for

seqs

character vector or XStringSet of sequences in which to search for and count occurrences of regex

overlap

logical value: should overlapping occurrences of regex be counted as multiple hits?

Value

if length(regex) is one, returns integer vector of counts; if length(regex) is more than one, returns matrix of counts: one row per sequence in seqs, one column per expression in regex

Examples

data(simulatedSeqs)
reCounts1 <- regexCounts('AAAAA|TTTTT', simulatedSeqs)
reCounts2 <- regexCounts(c('AAAAA|TTTTT', 'CG'), simulatedSeqs)


[Package sarks version 1.5.0 Index]