GeRnika (version 1.0.0)

calc_clone_proportions: Calculate clone proportions for a tumor

Description

This function calculates the proportions of each clone in a phylogenetic tree, following a given evolutionary mode (positive selection or neutral evolution).

Usage

calc_clone_proportions(B, selection)

Value

A data frame with two columns: 'clone_idx', which contains the clone identifiers, and 'proportion', which contains the calculated proportions of each clone.

Arguments

B

A matrix representing the mutation relationships between the nodes in the phylogenetic tree (B matrix).

selection

A character string representing the evolutionary mode the tumor follows. This should be either "positive" or "neutral".

Examples

# Calculate clone proportions for a tumor phylogenetic tree represented by a B matrix 
# and following a positive selection model

# Create a mutation matrix for a phylogenetic tree with 10 nodes and k = 2
B_mat <- create_B(10, 2)

# Calculate the clone proportions following a positive selection model
clone_proportions <- calc_clone_proportions(B_mat, "positive")