Summarize phyloseq data into a higher phylogenetic level.

aggregate_taxa(x, level, verbose = FALSE)

Arguments

x

phyloseq-class object

level

Summarization level (from rank_names(pseq))

verbose

verbose

Value

Summarized phyloseq object

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.

References

See citation('microbiome')

Author

Contact: Leo Lahti microbiome-admin@googlegroups.com

Examples

data(caporaso)
caporaso_phylum <- aggregate_taxa(caporaso, "Phylum")