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

Description Usage Arguments Value Examples

View source: R/taxonomy.R

Description

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

Usage

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assignSpecies(seqs, refFasta, allowMultiple = FALSE, verbose = FALSE)

Arguments

seqs

(Required). A character vector of the sequences to be assigned, or an object coercible by getUniques.

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.

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

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## Not run: 
 taxa <- assignSpecies(dadaF, "rdp_species.fa.gz")

## End(Not run)

Bioconductor-mirror/dada2 documentation built on June 1, 2017, 7:31 a.m.