getlikelihood

tree


    alternative allele read depth matrix


    observed standard deviation of major copy number (scalar input is
    transformed into matrix)

epsilonM


    observed standard deviation of minor copy number (scalar input is
    transformed into matrix)

epsilonm


To get likelihood of the tree given tree struture and data input. Used in
<code><a rd-options="" href="/link/canopy.sample?package=Canopy&version=1.0.0" data-mini-rdoc="Canopy::canopy.sample">canopy.sample</a></code>.


 package

A statistical framework and computational procedure for identifying the sub-populations within a tumor, determining the mutation profiles of each subpopulation, and inferring the tumor's phylogenetic history. The input are variant allele frequencies (VAFs) of somatic single nucleotide alterations (SNAs) along with allele-specific coverage ratios between the tumor and matched normal sample for somatic copy number alterations (CNAs). These quantities can be directly taken from the output of existing software. Canopy provides a general mathematical framework for pooling data across samples and sites to infer the underlying parameters. For SNAs that fall within CNA regions, Canopy infers their temporal ordering and resolves their phase.  When there are multiple evolutionary configurations consistent with the data, Canopy outputs all configurations along with their confidence assessment.

getlikelihood: To get likelihood of the tree

Description

Usage

Arguments

Value

Examples