aggregate_top_taxa {microbiome}R Documentation

Aggregate Top Taxa

Description

Summarize phyloseq data by combining the most abundant taxa.

Usage

aggregate_top_taxa(x, top, level)

Arguments

x

phyloseq-class object

top

Keep the top-n taxa, and merge the rest under the category 'Other'. Instead of top-n numeric this can also be a character vector listing the groups to combine.

level

Summarization level (from rank_names(pseq))

Value

phyloseq-class object

Author(s)

Contact: Leo Lahti microbiome-admin@googlegroups.com

References

See citation('microbiome')

Examples

data(dietswap)
s <- aggregate_top_taxa(dietswap, top = 3, 'Phylum')

[Package microbiome version 1.6.0 Index]