where2trim: Select position where a pattern has been found

In carlopacioni/amplicR: An R package to process amplicon data

Select position where a pattern has been found

Description

Takes a set of sequences and the output from Biostrings::vmatchPattern() and identify the first positions after the match with a pattern

Usage

where2trim(mismatch, subjectSet, patt_hits, patt, type = "F")

Arguments

mismatch	The number of allowed mismatches
subjectSet	The set of sequences that were used for the search
patt_hits	The output from Biostrings::vmatchPattern()
patt	The patter used for the search
type	The type of match, either forward "F", or reverse "R"

Details

This function is used internally by amplicR

Value

A list with start positions

carlopacioni/amplicR documentation built on Aug. 19, 2023, 7:59 p.m.