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, ...)

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.
...	Other arguments pass on to dada2::assignTaxonomy.

Value

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

Author(s)

Adrien Taudière

adrientaudiere/MiscMetabar documentation built on July 6, 2024, 7:02 p.m.