add_lowest_rank: Adds 'lowest_rank' to a phyloseq object

In DanielSprockett/reltools: Microbiome Amplicon Analysis and Visualization

Description

Adds a lowest_rank column to a taxonomy table in a phyloseq object.

Usage

add_lowest_rank(ps)

Arguments

ps	A phyloseq object that contains a tax_table

Value

This function returns the input phyloseq object with a lowest_rank column in the tax_table(). If "Species" is present in the tax_table(), then this function returns <Genus_species>. If "Species" is NA, this function returns the next highest taxonomic level available. If more than 1 "Species" is present, this function returns <Genus_species1/species2+nspecies>.

Examples

ps <- add_lowest_rank(ps)

DanielSprockett/reltools documentation built on May 5, 2019, 12:27 p.m.