GeRnika (version 1.1.0)

create_F: 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)

Value

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

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`.

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)