add_new_taxonomy_pq: Add new taxonomic rank to a phyloseq object.

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Add new taxonomic rank to a phyloseq object.

Description

One of main use of this function is to add taxonomic assignment from a new database.

Usage

add_new_taxonomy_pq(physeq, ref_fasta, suffix = NULL, method = "dada2", ...)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
ref_fasta	(required) A link to a database. Pass on to dada2::assignTaxonomy.
suffix	(character) The suffix to name the new columns. If set to NULL (the default), the basename of the file reFasta is used with the name of the method. Set suffix to "" in order to remove any suffix.
method	(required, default "dada2") :.add "dada2" : dada2::assignTaxonomy() "sintax" : see assign_sintax() "lca" : see assign_vsearch_lca()
...	Other arguments pass on to the taxonomic assignation method.

Value

A new phyloseq-class object with a larger slot tax_table"

Author(s)

Adrien Taudière

See Also

dada2::assignTaxonomy(), assign_sintax(), assign_vsearch_lca()

adrientaudiere/MiscMetabar documentation built on Dec. 19, 2024, 3:16 a.m.