documentation_rank.2

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_rank.2 function

<dl><dt>rank</dt>
<dd>What rank(s) of taxa to compute biplot coordinates and
statistics for, or <code>NULL</code> to disable. E.g. <code>"Phylum"</code>,
<code>"Genus"</code>, <code>".otu"</code>, etc. An integer vector 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>2</code>.</dd></dl>

Arguments

documentation_rank.2 — documentation_rank.2

<dl>

<dt>rank</dt>
<dd>What rank(s) of taxa to compute biplot coordinates and
statistics for, or <code>NULL</code> to disable. E.g. <code>"Phylum"</code>,
<code>"Genus"</code>, <code>".otu"</code>, etc. An integer vector 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>2</code>.</dd>

</dl>

documentation_rank.2: documentation_rank.2

Description

Arguments