import_mothur_constaxonomy

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

mothur_constaxonomy_file

(Optional). A specific function used
  for parsing the taxonomy string. See
  <code><a rd-options="" href="/link/parse_taxonomy_default?package=phyloseq&version=1.12.2" 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 rd-options="" href="/link/parse_taxonomy_greengenes?package=phyloseq&version=1.12.2" 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 J McMurdie

phyloseq

Handling and analysis of high-throughput microbiome
census data.

import_mothur_constaxonomy function

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

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

import_mothur_constaxonomy: Import mothur constaxonomy file and return a taxonomyTable

Description

Usage

Arguments

Value

See Also