get_revolver_pathways: Compute REVOLVER pathway probabilities

In cbg-ethz/TreeMHN: Joint inference of repeated evolutionary trajectories and patterns of clonal exclusivity from single-cell mutation trees

Compute REVOLVER pathway probabilities

Description

This function computes the pathway probabilities inferred from the row-normalized W matrix of the REVOLVER algorithm

Usage

get_revolver_pathways(n, tree_df, n_order = 4)

Arguments

n	Number of mutational events.
tree_df	A data frame with the following columns: Tree_ID: IDs of mutation trees, unique for each patient Node_ID: IDs of each node in the tree, including the root node (with ID "1"), unique for each node Mutation_ID: IDs of each mutational event, the root node has a mutation ID of "0", other mutation IDs can be duplicated in the tree to allow for parallel mutations Parent_ID: IDs of the parent node ID. The root node has itself as parent (ID "1").
n_order	Length of the pathways (Default: 4).

Value

A list containing the matrix W and the pathway probabilities inferred from the row-normalized W matrix of the REVOLVER algorithm.

Author(s)

Xiang Ge Luo

cbg-ethz/TreeMHN documentation built on Jan. 29, 2024, 1:29 p.m.