phyloseq_sep_tax: Split phyloseq object by taxonomic rank.
In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

phyloseq_sep_tax

R Documentation

Split phyloseq object by taxonomic rank.

Description

This function splits a phyloseq object by a specified taxonomic rank, returning a list of objects whose components each correspond to a taxonomic rank.

Usage

phyloseq_sep_tax(physeq, TaxRank = "Phylum", drop_NA = FALSE)

Arguments

`physeq`	A phyloseq-class object
`TaxRank`	Taxonomy rank name (e.g., "Phylum")
`drop_NA`	Logical, remove ranks with NAs

Value

List of phyloseq objects

Examples

data(GlobalPatterns)
# Subset data
GP <- subset_taxa(GlobalPatterns, Phylum %in% c("Acidobacteria", "Actinobacteria", "Firmicutes", "Verrucomicrobia"))
phyloseq_sep_tax(GP, TaxRank = "Phylum")

vmikk/metagMisc documentation built on Feb. 14, 2024, 2:29 a.m.