Simulation, Visualization and Comparison of Tumor Evolution Data

---

Documentation for package ‘GeRnika’ version 1.1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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