Description Usage Arguments Value Examples
assignSpecies
uses exact matching against a reference fasta to identify the
genus-species binomial classification of the input sequences.
1 2 3 4 5 6 7 8 | assignSpecies(
seqs,
refFasta,
allowMultiple = FALSE,
tryRC = FALSE,
n = 2000,
verbose = FALSE
)
|
seqs |
(Required). A character vector of the sequences to be assigned, or an object
coercible by |
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 |
verbose |
(Optional). Default FALSE. If TRUE, print status to standard output. |
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.
1 2 3 | 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)
|
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