input_tree_df: Process a dataframe of mutation trees and output a TreeMHN...

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

Process a dataframe of mutation trees and output a TreeMHN object

Description

This function processes a dataframe of mutation trees and output a TreeMHN object.

Usage

input_tree_df(
  n,
  tree_df,
  patients = NULL,
  tree_labels = NULL,
  mutations = NULL,
  weights = NULL
)

Arguments

n	Number of mutational events.
tree_df	A data frame with the following columns: Patient_ID: IDs of patients, unique for each patient Tree_ID: IDs of mutation trees, unique for each tree 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").
patients	A list of patient labels, which must be unique values. If no labels are given, then the patient IDs will be used.
tree_labels	A list of tree labels, which must be unique values. If no labels are given, then the tree IDs will be used.
mutations	A list of mutation names, which must be unique values. If no names are given, then the mutation IDs will be used.
weights	Weights of the trees. If no values are given, weights are assigned equally to the trees such that each patient has a weight of 1.

Value

A TreeMHN object

Author(s)

Xiang Ge Luo

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