Summarize phyloseq data into a higher phylogenetic level.
aggregate_taxa(x, level, verbose = FALSE)phyloseq-class object
Summarization level (from rank_names(pseq))
verbose
Summarized phyloseq object
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.
See citation('microbiome')
data(caporaso)
caporaso_phylum <- aggregate_taxa(caporaso, "Phylum")