phyloseq: get_taxa_unique – R documentation

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get_taxa_unique

Get a unique vector of the observed taxa at a particular taxonomic rank

Description

This is a simple accessor function to make it more convenient to determine the different taxa present for a particular taxonomic rank in a given phyloseq-class object.

Usage

get_taxa_unique(physeq, taxonomic.rank=rank_names(physeq)[1], errorIfNULL=TRUE)

Arguments

`physeq`	(Required). `taxonomyTable-class`, or `phyloseq-class`.
`taxonomic.rank`	(Optional). Character. The taxonomic rank to use. Must select from the set indicated by `get_taxa_unique`. Default is to take the first column of the `taxonomyTable` component.
`errorIfNULL`	(Optional). Logical. Should the accessor stop with an error if the slot is empty (`NULL`)? Default `TRUE`.

Value

Character vector. Unique vector of the observed taxa at a particular taxonomic rank

Examples

data(enterotype)
get_taxa_unique(enterotype)
data(GlobalPatterns)
get_taxa_unique(GlobalPatterns, "Family")

phyloseq

Handling and analysis of high-throughput microbiome census data

v1.34.0

AGPL-3

Authors

Paul J. McMurdie <joey711@gmail.com>, Susan Holmes <susan@stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain

Initial release

2019-04-23