import_mothur_otu_table

The list file name and/or
 location as produced by mothur.

mothur_list_file

The name/location of the group
 file produced by mothur's <code>make.group()</code>
 function. It contains information about the sample source
 of individual sequences, necessary for creating a
 species/taxa abundance table (<code>otu_table</code>). See
 <code>http://www.mothur.org/wiki/Make.group</code>

mothur_group_file

A character string indicating the cutoff
 value, (or <code>"unique"</code>), that matches one of the
 cutoff-values used to produce the OTU clustering results
 contained within the list-file created by mothur
 (and specified by the <code>mothur_list_file</code> argument).
 The default is to take the largest value among the cutoff
 values contained in the list file. If only one cutoff is
 included in the file, it is taken and this argument does
 not need to be specified. Note that the <code>cluster()</code>
 function within the mothur package will often
 produce a list file with multiple cutoff values, even if
 a specific cutoff is specified. It is suggested that you
 check which cutoff values are available in a given list
 file using the <code><a rd-options="" href="/link/show_mothur_cutoffs?package=phyloseq&version=1.12.2" data-mini-rdoc="phyloseq::show_mothur_cutoffs">show_mothur_cutoffs</a></code>
 function.

cutoff


  Import mothur list and group files and return an
  otu_table


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_otu_table function

A character string indicating the cutoff
 value, (or <code>"unique"</code>), that matches one of the
 cutoff-values used to produce the OTU clustering results
 contained within the list-file created by mothur
 (and specified by the <code>mothur_list_file</code> argument).
 The default is to take the largest value among the cutoff
 values contained in the list file. If only one cutoff is
 included in the file, it is taken and this argument does
 not need to be specified. Note that the <code>cluster()</code>
 function within the mothur package will often
 produce a list file with multiple cutoff values, even if
 a specific cutoff is specified. It is suggested that you
 check which cutoff values are available in a given list
 file using the <code><a rd-options='' href='show_mothur_cutoffs'>show_mothur_cutoffs</a></code>
 function.

import_mothur_otu_table: Import mothur list and group files and return an otu_table

Description

Usage

Arguments

Value

See Also