assignSpecies: Taxonomic assignment to the species level by exact matching.

In benjjneb/dada2: Accurate, high-resolution sample inference from amplicon sequencing data

Taxonomic assignment to the species level by exact matching.

Description

assignSpecies uses exact matching against a reference fasta to identify the genus-species binomial classification of the input sequences.

Usage

assignSpecies(
  seqs,
  refFasta,
  allowMultiple = FALSE,
  tryRC = FALSE,
  n = 2000,
  verbose = FALSE
)

Arguments

seqs	(Required). A character vector of the sequences to be assigned, or an object coercible by getUniques. Sequences must be A/C/G/T only.
refFasta	(Required). The path to the reference fasta file, or an R connection. Can be compressed. This reference fasta file should be formatted so that the id lines correspond to the genus-species of the associated sequence: >SeqID genus species ACGAATGTGAAGTAA......
allowMultiple	(Optional). Default FALSE. Defines the behavior when multiple exact matches against different species are returned. By default only unambiguous identifications are return. If TRUE, a concatenated string of all exactly matched species is returned. If an integer is provided, multiple identifications up to that many are returned as a concatenated string.
tryRC	(Optional). Default FALSE. If TRUE, the reverse-complement of each sequences will also be tested for exact matching to the reference sequences.
n	(Optional). Default 2000. The number of sequences to perform assignment on at one time. This controls the peak memory requirement so that large numbers of sequences are supported.
verbose	(Optional). Default FALSE. If TRUE, print status to standard output.

Value

A two-column character matrix. Rows correspond to the provided sequences, columns to the genus and species taxonomic levels. NA indicates that the sequence was not classified at that level.

Examples

seqs <- getSequences(system.file("extdata", "example_seqs.fa", package="dada2"))
species_fasta <- system.file("extdata", "example_species_assignment.fa.gz", package="dada2")
spec <- assignSpecies(seqs, species_fasta)

benjjneb/dada2 documentation built on Dec. 5, 2024, 4:02 p.m.