aggregate_taxa: Aggregate Taxa

In microbiome: Microbiome Analytics

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(dietswap)
s <- aggregate_taxa(dietswap, 'Phylum')

microbiome documentation built on Nov. 8, 2020, 5:08 p.m.