GeRnika (version 1.0.0)

create_U: Calculate tumor clone frequencies in samples

Description

This function calculates the frequencies of each clone in a set of samples, given the global clone proportions in the tumor and their spatial distribution.

Usage

create_U(B, clone_proportions, density_coords, m, x)

Value

A matrix where each row corresponds to a sample, and each column corresponds to a clone. The value at the i-th row and j-th column is the frequency of the j-th clone in the i-th sample.

Arguments

B

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

clone_proportions

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

density_coords

A data frame where each column represents the density of a clone at different spatial coordinates.

m

An integer representing the number of samples taken from the tumor.

x

A numeric vector representing the spatial coordinates.

Examples

# Calculate the frequencies of each clone in 10 samples taken from a tumor represented by the B 
# matrix B_mat, with global clone proportions clone_proportions, spatial distribution 
# density_coords, and spatial coordinates x

# Create random topology
B <- create_B(20, 3)

# Assign proportions to each clone following a neutral evolution model
clone_proportions <- calc_clone_proportions(B, "neutral")

# Place clones in 1D space
clones_space <- place_clones_space(B)
density_coords <- clones_space$spatial_coords
domain <- clones_space$x

# Create U matrix with parameter m=4
U <- create_U(B = B, clone_proportions = clone_proportions, 
              density_coords = density_coords, m = 4, x = domain)