select_taxa-methods: Select a subset of taxa in a specified order where possible

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Select a subset of taxa in a specified order where possible

Description

Select (a subset of) taxa; if x allows taxa to be reordered, then taxa are given in the specified order.

Usage

select_taxa(x, taxa, reorder = TRUE)

## S4 method for signature 'sample_data,character'
select_taxa(x, taxa)

## S4 method for signature 'otu_table,character'
select_taxa(x, taxa, reorder = TRUE)

## S4 method for signature 'taxonomyTable,character'
select_taxa(x, taxa, reorder = TRUE)

## S4 method for signature 'XStringSet,character'
select_taxa(x, taxa, reorder = TRUE)

## S4 method for signature 'phylo,character'
select_taxa(x, taxa)

## S4 method for signature 'phyloseq,character'
select_taxa(x, taxa, reorder = TRUE)

Arguments

x	A phyloseq object or phyloseq component object
taxa	Character vector of taxa to select, in requested order
reorder	Logical specifying whether to use the order in taxa (TRUE) or keep the order in taxa_names(x) (FALSE)

Details

This is a simple selector function that is like prune_taxa(taxa, x) when taxa is a character vector but always gives the taxa in the order taxa if possible (that is, except for phy_tree's and phyloseq objects that contain phy_tree's).

Author(s)

Michael R. McLaren (orcid: 0000-0003-1575-473X)

MiscMetabar documentation built on Oct. 8, 2024, 1:07 a.m.