documentation_clusters

internal

A toolkit for working with Biological Observation Matrix ('BIOM') files.
Read/write all 'BIOM' formats. Compute rarefaction, alpha diversity, and
beta diversity (including 'UniFrac'). Summarize counts by taxonomic level.
Subset based on metadata. Generate visualizations and statistical analyses.
CPU intensive operations are coded in C for speed.

Daniel P. Smith

rbiom

Read/Write, Analyze, and Visualize 'BIOM' Data

Alkek Center for Metagenomics and Microbiome Research 

documentation_clusters function

<dl><dt>k</dt>
<dd>Number of clusters. Default: <code>5L</code></dd>
<dt>rank</dt>
<dd>Which taxa rank to use. E.g. <code>"Phylum"</code>,
<code>"Genus"</code>, <code>".otu"</code>, etc. An integer can also be
given, where <code>1</code> is the highest rank, <code>2</code> is the second
highest, <code>-1</code> is the lowest rank, <code>-2</code> is the second
lowest, and <code>0</code> is the OTU "rank". Run <code>biom$ranks</code> to
see all options for a given rbiom object. Default: <code>.otu</code>.</dd></dl>

Arguments

documentation_clusters — documentation_clusters

<dl>

<dt>k</dt>
<dd>Number of clusters. Default: <code>5L</code></dd>


<dt>rank</dt>
<dd>Which taxa rank to use. E.g. <code>"Phylum"</code>,
<code>"Genus"</code>, <code>".otu"</code>, etc. An integer can also be
given, where <code>1</code> is the highest rank, <code>2</code> is the second
highest, <code>-1</code> is the lowest rank, <code>-2</code> is the second
lowest, and <code>0</code> is the OTU "rank". Run <code>biom$ranks</code> to
see all options for a given rbiom object. Default: <code>.otu</code>.</dd>

</dl>

documentation_clusters: documentation_clusters

Description

Value

Arguments