import_mothur_constaxonomy

(Required). A 
<href>http://www.mothur.org/wiki/Constaxonomy_file</href>{consensus taxonomy file} 
produced by <em>mothur</em>.

mothur_constaxonomy_file

(Optional). A specific function used for parsing the taxonomy string.
See <code><a href="/link/parse_taxonomy_default?package=phyloseq&version=1.16.2" rd-options="" data-mini-rdoc="phyloseq::parse_taxonomy_default">parse_taxonomy_default</a></code> 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 (<code><a href="/link/parse_taxonomy_greengenes?package=phyloseq&version=1.16.2" rd-options="" data-mini-rdoc="phyloseq::parse_taxonomy_greengenes">parse_taxonomy_greengenes</a></code>).

parseFunction

Import mothur constaxonomy file and return a taxonomyTable

internal

phyloseq provides a set of classes and tools
    to facilitate the import, storage, analysis, and
    graphical display of microbiome census data.

Paul McMurdie

phyloseq

Handling and analysis of high-throughput microbiome
    census data

import_mothur_constaxonomy function

(Optional). A specific function used for parsing the taxonomy string.
See <code><a href="parse_taxonomy_default" rd-options="">parse_taxonomy_default</a></code> 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 (<code><a href="parse_taxonomy_greengenes" rd-options="">parse_taxonomy_greengenes</a></code>).

import_mothur_constaxonomy: Import mothur constaxonomy file and return a taxonomyTable

Description

Usage

Arguments

Value

See Also