classify_taxa: (Re)classify amplicon sequences

In SWittouck/tidyamplicons: Functions to Manipulate and Visualize Amplicon Abundance Data

(Re)classify amplicon sequences

Description

This function requires the DADA2 package to be installed.

Usage

classify_taxa(
  ta,
  refdb,
  taxa = rep(T, times = length(taxon_id)),
  ranks = "default",
  sequence_var = "sequence",
  multithread = T,
  min_boot = 50,
  n_ranks = 7
)

Arguments

ta	A tidyamplicons object.
refdb	The path to a DADA2-compatible reference database.
taxa	An expression that specifies which taxa to (re)classify.
ranks	A vector that specifies which ranks to (re)classify.
sequence_var	The (quoted) name of a variable within the taxa table that contains (representative) sequences of the taxa.
multithread	A boolean indicating whether to use multiple threads.
min_boot	The minimum bootstrap value for taxonomy assignment.
n_ranks	The number of ranks present in the reference database.

Details

This function will (re)classify either all or a subset of the taxa, given that a variable is present in the taxon table that contains (representative) sequences of the taxa.

Ranks can be supplied as a named integer vector, where the names represent taxonomic ranks and the integers represent positions of these ranks in the taxonomy strings present in the reference database. Ranks can also be supplied as just a character vector with the rank names; in that case, it is assumed that the database taxonomy string follows the default order domain, phylum, class, order, family, genus, species. If no ranks are supplied, taxa will be (re)classified at all default ranks.

Value

An updated tidyamplicons object.

SWittouck/tidyamplicons documentation built on Aug. 15, 2023, 3:14 a.m.