# Simulation, Visualization and Comparison of Tumor Evolution Data

## Documentation for package ‘GeRnika’ version 1.2.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

add_noise | Add noise to the VAF values in an F matrix
B_mats | A set of 10 trios of B matrices for experimenting with the methods of 'GeRnika'
B_to_phylotree | Create a 'Phylotree' object from a 'B' matrix.
combine_trees | Get consensus tree between two phylogenetic trees
create_B | Create tumor phylogenetic tree topology
create_F | Calculate the variant allele frequency (VAF) values in a set of samples
create_instance | Create a tumor phylogenetic tree instance
create_phylotree | Create a 'Phylotree' object
create_U | Calculate tumor clone frequencies in samples
equals | Check if two phylogenetic trees are equal
find_common_subtrees | Find the set of common subtrees between two phylogenetic trees
palettes | Palettes for the methods of 'GeRnika'
Phylotree-class | S4 class to represent phylogenetic trees.
plot | Plot a Phylotree object.
plot-method | Plot a Phylotree object.
plot_proportions | Plot a phylogenetic tree with proportional node sizes and colors