summarize_taxa: summarize_taxa

In jbisanz/qiime2R: qiime2R

summarize_taxa

Description

Takes a feature table (ex OTUs/SVs) and a parsed taxonomy table to generate a named list of feature tables with abundances summed to each taxonomic level.

Usage

summarize_taxa(features, taxonomy)

Arguments

features	a table of abundances where rows are features and columns are samples
taxonomy	a table of taxonomies that has been parsed (ex using parse_taxonomy). Should contain the following columns: Kingdom,Phylum,Class,Order,Family,Genus,Species.

Value

a named list of abundances aggregated at each level.

Examples

## Not run: taxasums<-summarize_taxa(svtable, taxonomy); taxasums$Species

jbisanz/qiime2R documentation built on Dec. 17, 2024, 4:09 p.m.