get_taxa_unique: Get a unique vector of the observed taxa at a particular...

In joey711/phyloseq: Handling and analysis of high-throughput microbiome census data

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

See Also

get_taxa taxa_names sample_names

Examples

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

joey711/phyloseq documentation built on Nov. 4, 2022, 1:16 a.m.