assignSpecies {dada2} | R Documentation

## 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`.
`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)

[Package dada2 version 1.18.0 Index]