Man pages for cbg-ethz/TreeMHN
Joint inference of repeated evolutionary trajectories and patterns of clonal exclusivity from single-cell mutation trees
| compare_Theta | Compute the differences between two Mutual Hazard Networks |
| generate_trees | Generate a set of trees based on a Mutual Hazard Network |
| get_hintra_pathways | Compute HINTRA pathway probabilities |
| get_MC_flags | get_MC_flags(N, trees) A function that determines whether... |
| get_revolver_pathways | Compute REVOLVER pathway probabilities |
| initialize_Theta | initialize_Theta(n, N, trees, lambda_s) A function that... |
| input_tree_df | Process a dataframe of mutation trees and output a TreeMHN... |
| KL_divergence | Compute the KL divergence between two probability... |
| learn_MHN | Learn a Mutual Hazard Network from a set of mutation trees |
| output_tree_df | output_tree_df(tree_obj) A helper function that construct a... |
| plot_next_mutations | Plot the next most probable mutational events |
| plot_observed_pathways | Plot most frequent observed pathways from a cohort of... |
| plot_pathways | Plot most probable pathways of a given length computed from a... |
| plot_pathways_w_sampling | Plot most probable pathways before a sampling event computed... |
| plot_Theta | Plot a Mutual Hazard Network |
| plot_tree_df | Plot a tree in data frame format |
| plot_tree_list | Plot a tree in named list format |
| random_Theta | random_Theta(n, sparsity, exclusive_ratio) This function... |
| sort_one_tree_df | tree_df_to_trees(one_tree_df) A helper function that sorts... |
| Theta_to_pathways | Compute the pathway probabilities given a Mutual Hazard... |
| tree_df_to_genotypes | tree_df_to_genotypes(n, tree_df) This function processes a... |
| tree_df_to_trees | tree_df_to_trees(n, tree_df) This function processes a data... |
| trees_to_revolver_W | trees_to_revolver_W(n, tree_df) This function computes the... |
