phylotax_to_phyloseq: Convert assigned taxonomy and tree to a phyloseq object

In brendanf/phylotax: Refine taxonomic assignment of environmental sequences using a taxonomic tree

Description

The output will have tax_table defined based on the assigned taxa in phylotax, and phy_tree defined based on the tree in phylotax, if one is present.

Usage

phylotax_to_phyloseq(phylotax, otu_table, ..., use_tree = TRUE)

Arguments

phylotax	(phylotax object)
otu_table	(phyloseq::otu_table object)
...	Additional arguments to pass to phyloseq::phyloseq(). These should generally be the result of phyloseq::sample_data(), but could also include a phylo object if phylotax does not already have one or if use_tree=FALSE.
use_tree	(logical) If FALSE, do not use the tree from phylotax even if one exists.

Details

The resulting object will contain all taxon labels found in both otu_table and the tree associated with phylotax, if any. Taxon labels with no assignments in phylotax will have NA for all ranks in the output's taxonomy table.

Value

A phyloseq::phyloseq object.

brendanf/phylotax documentation built on March 3, 2021, 2:21 p.m.