Simulation, Visualization and Comparison of Tumor Evolution Data


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Documentation for package ‘GeRnika’ version 1.0.0

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.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