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 href="/link/show_mothur_cutoffs?package=phyloseq&version=1.16.2" rd-options="" 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 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 href="show_mothur_cutoffs" rd-options="">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