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 |