aggregate_top_taxa2: Aggregate Top Taxa v2

In microsud/microbiomeutilities: microbiomeutilities: Utilities for Microbiome Analytics

Aggregate Top Taxa v2

Description

Summarize phyloseq: combine other than the most abundant taxa.

Usage

aggregate_top_taxa2(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))

Details

Backup from microbiome R pkg. This function is replaced by aggregate_rare function.

Value

phyloseq-class object

Author(s)

Contact: Leo Lahti [e-mail]

References

See citation('microbiome')

Examples

data(dietswap)
s <- aggregate_top_taxa2(dietswap, top = 3, "Phylum")

microsud/microbiomeutilities documentation built on Nov. 29, 2022, 12:18 a.m.