aggregate_taxa {microbiome} | R Documentation

## Aggregate Taxa

### Description

Summarize phyloseq data into a higher phylogenetic level.

### Usage

    aggregate_taxa(x, level, top = NULL)

### Arguments

`x` | `phyloseq-class` object
`level` | Summarization level (from `rank_names(pseq)`)
`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.

### 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

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

[Package microbiome version 1.2.1 Index]