aggregate_taxa: Aggregate Taxa

View source: R/process_aggregate_taxa.R

aggregate_taxaR Documentation

Aggregate Taxa

Description

Summarize phyloseq data into a higher phylogenetic level.

Usage

aggregate_taxa(x, level, verbose = FALSE)

Arguments

x

phyloseq-class object

level

Summarization level (from rank_names(pseq))

verbose

verbose

Details

This provides a convenient way to aggregate phyloseq OTUs (or other taxa) when the phylogenetic tree is missing. Calculates the sum of OTU abundances over all OTUs that map to the same higher-level group. Removes ambiguous levels from the taxonomy table. Returns a phyloseq object with the summarized abundances.

Value

Summarized phyloseq object

Author(s)

Contact: Leo Lahti microbiome-admin@googlegroups.com

References

See citation('microbiome')

Examples

data(caporaso)
caporaso_phylum <- aggregate_taxa(caporaso, "Phylum")


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