parse_taxonomy: Parse Q2 taxonomy

View source: R/parse_taxonomy.R

parse_taxonomyR Documentation

Parse Q2 taxonomy

Description

Parse Q2 taxonomy

Usage

parse_taxonomy(taxonomy, tax_sep, trim_extra)

Arguments

taxonomy

a table-like object containing the columns Feature.ID and Taxon. Can be imported using read_qza(file)$data.

tax_sep

The separator between taxonomic levels. Defaults to one compatible with both GreenGenes and SILVA ("; " OR ";")

trim_extra

Remove leading characters from taxonomic levels: ex: k__ or D_0__. TRUE/FALSE. default=TRUE

Note: Assumes an assignment has been made to all levels. Fills missing assignments with NA.

Value

a data.frame with feature IDs as row names and the columns: Kingdom, Phylum, Class, Order, Family, Genus, Species

Examples

## Not run: taxonomy<-parse_taxonomy(taxonomy)

jbisanz/qiime2R documentation built on April 24, 2024, 5 p.m.