write.biom

The BIOM object to save to the file.

biom

file

Options are &#8220;tab&#8221;, 
&#8220;json&#8221;, and &#8220;hdf5&#8221;, 
corresponding to classic tabular format, biom format version 1.0 and 
biom version 2.1, respectively. Abbreviations are also accepted. See
<a href="http://biom-format.org/documentation/">http://biom-format.org/documentation/</a> for details. NOTE: to write
HDF5 formatted BIOM files, the BioConductor R package <code>rhdf5</code> must
be installed.

format

Write counts, metadata, taxonomy, and phylogeny to a biom file.

A toolkit for working with Biological Observation Matrix ('BIOM') files.
Features include reading/writing all 'BIOM' formats, rarefaction, alpha
diversity, beta diversity (including 'UniFrac'), summarizing counts by
taxonomic level, and sample subsetting. Standalone functions for
reading, writing, and subsetting phylogenetic trees are also provided.
All CPU intensive operations are encoded in C with multi-thread support.

Daniel P. Smith

rbiom

Read/Write, Transform, and Summarize 'BIOM' Data

write.biom function

<dl><dt>biom</dt>
<dd>The BIOM object to save to the file.</dd>
<dt>file</dt>
<dd>Path to the output file.</dd>
<dt>format</dt>
<dd>Options are &#8220;tab&#8221;, 
&#8220;json&#8221;, and &#8220;hdf5&#8221;, 
corresponding to classic tabular format, biom format version 1.0 and 
biom version 2.1, respectively. Abbreviations are also accepted. See
<a href="http://biom-format.org/documentation/">http://biom-format.org/documentation/</a> for details. NOTE: to write
HDF5 formatted BIOM files, the BioConductor R package <code>rhdf5</code> must
be installed.</dd></dl>

Arguments

Write counts, metadata, taxonomy, and phylogeny to a biom file. — write.biom

<dl>

<dt>biom</dt>
<dd>The BIOM object to save to the file.</dd>


<dt>file</dt>
<dd>Path to the output file.</dd>


<dt>format</dt>
<dd>Options are &#8220;tab&#8221;, 
&#8220;json&#8221;, and &#8220;hdf5&#8221;, 
corresponding to classic tabular format, biom format version 1.0 and 
biom version 2.1, respectively. Abbreviations are also accepted. See
<a href='http://biom-format.org/documentation/'>http://biom-format.org/documentation/</a> for details. NOTE: to write
HDF5 formatted BIOM files, the BioConductor R package <code>rhdf5</code> must
be installed.</dd>

</dl>

write.biom: Write counts, metadata, taxonomy, and phylogeny to a biom file.

Description

Usage

Value

Arguments