create_F: Calculate the variant allele frequency (VAF) values in a set...

In GeRnika: Simulation, Visualization and Comparison of Tumor Evolution Data

Calculate the variant allele frequency (VAF) values in a set of samples

Description

This method generates the F matrix that contains the mutation frequency values of a series of mutations in a collection of tumor biopsies or samples.

Usage

create_F(U, B, heterozygous = TRUE)

Arguments

U	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.
B	A matrix representing the mutation relationships between the nodes in the phylogenetic tree.
heterozygous	A logical value indicating whether to adjust the clone proportions for heterozygous states. If 'TRUE', the clone proportions are halved. If 'FALSE', the clone proportions are not adjusted. Default is 'TRUE'.

Value

A matrix containing the VAF values of a series of mutations in a set of samples.

Examples

# Create random topology with 10 nodes and k = 2
B <- create_B(10, 2)

# Create U matrix with parameter m=4 and "positive" selection
U <- create_U(B = B, m = 4, selection = "positive")

# Then we compute the F matrix for a heterozygous tumor
F <- create_F(U = U, B = B, heterozygous = TRUE)

GeRnika documentation built on April 3, 2025, 7:48 p.m.