Simulation, Visualization and Comparison of Tumor Evolution Data


[Up] [Top]

Documentation for package ‘GeRnika’ version 1.1.0

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