Tree

Reconstruction of the tumor phylogenetic tree
Generated by :
 Tree&lt;-Tree_generation(cbind(QuantumClone::QC_output$EM.output$centers[[1]],
 QuantumClone::QC_output$EM.output$centers[[2]]))

datasets

Using HTS data, clusters mutations in order to recreate putative
clones from the data provided. It requires genotype at the location of the
variant as well as the depth of coverage and number of reads supporting the
mutation. Additional information may be provided, such as the contamination
in the tumor sample. This package also provides a function QuantumCat() which
simulates data obtained from tumor sequencing.

Paul Deveau

QuantumClone

Clustering Mutations using High Throughput Sequencing (HTS) Data

Tree function

list of lists<dl class="dl-horizontal">
 <dt>Top level</dt><dd>List of all possibilities</dd>
 <dt>dataframe</dt><dd>Table of hierarchical relations</dd>
 <dt>numeric</dt><dd>probability of this tree</dd>
</dl>

Format

Example of output by Tree_generation — Tree

list of lists<dl class='dl-horizontal'>
 <dt>Top level</dt><dd>List of all possibilities</dd>
 <dt>dataframe</dt><dd>Table of hierarchical relations</dd>
 <dt>numeric</dt><dd>probability of this tree</dd>
</dl>

Tree: Example of output by Tree_generation

Description

Usage

Arguments

Format