parse_taxonomy: Parse Q2 taxonomy

In jbisanz/qiime2R: qiime2R

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 Dec. 17, 2024, 4:09 p.m.