aggregate_taxa: Aggregate Taxa

Description Usage Arguments Details Value Author(s) References Examples

View source: R/aggregate_taxa.R

Description

Summarize phyloseq data into a higher phylogenetic level.

Usage

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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

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