Simulation, Visualization and Comparison of Tumor Evolution Data

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Documentation for package ‘GeRnika’ version 1.0.0

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

Help Pages

.distribute_freqs	Distribute frequencies among clone and its children clones
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.
calc_clone_proportions	Calculate clone proportions for a tumor
combine_trees	Get consensus tree between two phylogenetic trees
create_B	Create tumor phylogenetic tree topology
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
get_clones	Retrieve the clone indices for a set of gene indices
get_genes	Retrieve the gene indices for the clones in a phylogenetic tree
get_parents	Get parent nodes in a phylogenetic tree.
hyperparameters	Hyperparameters for the methods of 'GeRnika'
Node-class	S4 class to represent a node in a phylogenetic tree.
palettes	Palettes for the methods of 'GeRnika'
Phylotree-class	S4 class to represent phylogenetic trees.
phylotree_to_B	Get B matrix from 'Phylotree' object.
phylotree_to_tree	Extract tree from 'Phylotree' object.
place_clones_space	Create a model for the spatial distribution of the clones in a tumor
plot	Plot a Phylotree object.
plot-method	Plot a Phylotree object.
plot_p	Plot a phylogenetic tree with proportional node sizes and colors.
plot_phylotree	Plot a phylogenetic tree
plot_proportions	Plot a phylogenetic tree with proportional node sizes and colors