search_exact_seq_pq: Search for exact matching of sequences
In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

search_exact_seq_pq

R Documentation

Search for exact matching of sequences

Description

Search for exact matching of sequences using complement, reverse and reverse-complement

Usage

search_exact_seq_pq(physeq, seq2search)

Arguments

`physeq`	(required): a `phyloseq-class` object obtained using the `phyloseq` package.
`seq2search`	A DNAStringSet object of sequences to search for.

Value

A list of data-frames for each input sequences with the name, the sequences and the number of occurrences of the original sequence, the complement sequence, the reverse sequence and the reverse-complement sequence.

Author(s)

Adrien Taudière

Examples

data("data_fungi")
search_primers <- search_exact_seq_pq(data_fungi,
  seq2search = Biostrings::DNAStringSet(c("TTGAACGCACATTGCGCC", "ATCCCTACCTGATCCGAG"))
)

MiscMetabar documentation built on Oct. 8, 2024, 1:07 a.m.