Phylotree-class

S4 class to represent phylogenetic trees.

Simulating, visualizing and comparing tumor clonal data by using simple commands. This aims at providing a tool to help researchers to easily simulate tumor data and analyze the results of their approaches for studying the composition and the evolutionary history of tumors.

Aitor Sánchez-Ferrera

GeRnika

Simulation, Visualization and Comparison of Tumor Evolution Data

Maitena Tellaetxe-Abete

Borja Calvo

Phylotree-class function

<dl>
<dt><code>B</code></dt>
<dd>A data.frame containing the square matrix that represents the ancestral relations among the clones of the phylogenetic tree.</dd></dl>
<dt><code>clones</code></dt>
<dd>A vector representing the equivalence table of the clones in the phylogenetic tree.</dd>
<dt><code>genes</code></dt>
<dd>A vector representing the equivalence table of the genes in the phylogenetic tree.</dd>
<dt><code>parents</code></dt>
<dd>A vector representing the parents of the clones in the phylogenetic tree.</dd>
<dt><code>tree</code></dt>
<dd>A <code>Node</code> class object representing the phylogenetic tree.</dd>
<dt><code>labels</code></dt>
<dd>A vector representing the tags of the genes in the phylogenetic tree.</dd>

Slots

S4 class to represent phylogenetic trees. — Phylotree-class

<dl>
<dt><code>B</code></dt>
<dd>A data.frame containing the square matrix that represents the ancestral relations among the clones of the phylogenetic tree.</dd>


<dt><code>clones</code></dt>
<dd>A vector representing the equivalence table of the clones in the phylogenetic tree.</dd>


<dt><code>genes</code></dt>
<dd>A vector representing the equivalence table of the genes in the phylogenetic tree.</dd>


<dt><code>parents</code></dt>
<dd>A vector representing the parents of the clones in the phylogenetic tree.</dd>


<dt><code>tree</code></dt>
<dd>A <code>Node</code> class object representing the phylogenetic tree.</dd>


<dt><code>labels</code></dt>
<dd>A vector representing the tags of the genes in the phylogenetic tree.</dd>


</dl>

Phylotree-class: S4 class to represent phylogenetic trees.

Description

Arguments

Slots