import_mothur_constaxonomy: Import mothur constaxonomy file and return a taxonomyTable

In joey711/phyloseq: Handling and analysis of high-throughput microbiome census data

Import mothur constaxonomy file and return a taxonomyTable

Description

Import mothur constaxonomy file and return a taxonomyTable

Usage

import_mothur_constaxonomy(mothur_constaxonomy_file,
  parseFunction = parse_taxonomy_default)

Arguments

mothur_constaxonomy_file

(Required). A consensus taxonomy file produced by mothur.

parseFunction

(Optional). A specific function used for parsing the taxonomy string. See parse_taxonomy_default for an example. If the default is used, this function expects a semi-colon delimited taxonomy string, with no additional rank specifier. A common taxonomic database is GreenGenes, and for recent versions its taxonomy includes a prefix, which is best cleaved and used to precisely label the ranks (parse_taxonomy_greengenes).

Value

An taxonomyTable-class object.

See Also

import_mothur

tax_table

phyloseq

joey711/phyloseq documentation built on Nov. 4, 2022, 1:16 a.m.