summarize_taxa: Summarize taxa into a taxonomic level within each sample

In HuaZou/MicrobiomeAnalysis: Data analysis toolkits in metagenomics

Summarize taxa into a taxonomic level within each sample

Description

Provides summary information of the representation of a taxonomic levels within each sample.

Usage

summarize_taxa(ps, level = rank_names(ps)[1], absolute = TRUE, sep = "|")

Arguments

ps	a phyloseq-class object.
level	taxonomic level to summarize, default the top level rank of the ps.
absolute	logical, whether return the absolute abundance or relative abundance, default FALSE.
sep	a character string to separate the taxonomic levels.

Value

a phyloseq::phyloseq object, where each row represents a taxa, and each col represents the taxa abundance of each sample.

Examples

data(enterotypes_arumugam)
summarize_taxa(enterotypes_arumugam)

HuaZou/MicrobiomeAnalysis documentation built on May 13, 2024, 11:10 a.m.