aggregate_taxa: Aggregate Taxa

In HuaZou/MicrobiomeAnalysis: Data analysis toolkits in metagenomics

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 [e-mail]

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.