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<table width="100%" summary="page for cutreeDynamicTree {dynamicTreeCut}"><tr><td>cutreeDynamicTree {dynamicTreeCut}</td><td align="right">R Documentation</td></tr></table>
<h2>Dynamic dendrogram pruning based on dendrogram only</h2>
<h3>Description</h3>
<p>
Detect clusters in a hierarchical dendrogram using a variable cut height approach. Uses only the
information in the dendrogram itself is used (which may give incorrect assignment for outlying objects).
</p>
<h3>Usage</h3>
<pre>
cutreeDynamicTree(dendro, maxTreeHeight = 1, deepSplit = TRUE, minModuleSize = 50)
</pre>
<h3>Arguments</h3>
<table summary="R argblock">
<tr valign="top"><td><code>dendro</code></td>
<td>
Hierarchical clustering dendrogram such produced by <code><a href="../../stats/html/hclust.html">hclust</a></code>.</td></tr>
<tr valign="top"><td><code>maxTreeHeight</code></td>
<td>
Maximum joining height of objects to be considered part of clusters.</td></tr>
<tr valign="top"><td><code>deepSplit</code></td>
<td>
If <code>TRUE</code>, method will favor sensitivity and produce more smaller clusters. When
<code>FALSE</code>, there will be fewer bigger clusters.</td></tr>
<tr valign="top"><td><code>minModuleSize</code></td>
<td>
Minimum module size. Branches containing fewer than <code>minModuleSize</code> objects
will be left unlabeled.</td></tr>
</table>
<h3>Details</h3>
<p>
A variable height branch pruning technique for dendrograms produced by hierarchical clustering.
Initially, branches are cut off at the height <code>maxTreeHeight</code>; the resulting clusters are then
examined for substructure and if subclusters are detected, they are assigned separate labels. Subclusters
are detected by structure and are required to have a minimum of <code>minModuleSize</code> objects on them to
be assigned a separate label. A rough degree of control over what it means to be a subcluster is
implemented by the parameter <code>deepSplit</code>.
</p>
<h3>Value</h3>
<p>
A vector of numerical labels giving assignment of objects to modules. Unassigned objects are labeled 0,
the largest module has label 1, next largest 2 etc.</p>
<h3>Author(s)</h3>
<p>
Bin Zhang, <a href="mailto:binzhang.ucla@gmail.com">binzhang.ucla@gmail.com</a>, with contributions by Peter Langfelder,
<a href="mailto:Peter.Langfelder@gmail.com">Peter.Langfelder@gmail.com</a>.
</p>
<h3>References</h3>
<p>
<a href="http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting">http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting</a>
</p>
<h3>See Also</h3>
<p>
<code><a href="cutreeHybrid.html">cutreeHybrid</a></code>
</p>
<hr><div align="center">[Package <em>dynamicTreeCut</em> version 1.11-3 <a href="00Index.html">Index]</a></div>
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