add_noise: Add noise to the VAF values in an F matrix

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

Add noise to the VAF values in an F matrix

Description

This function adds noise to the variant allele frequency (VAF) values in an F matrix, simulating the effect of sequencing errors. The noise is modeled as a negative binomial distribution for the depth of the reads and a binomial distribution for both the variant allele counts and the mismatch counts.

Usage

add_noise(F_matrix, depth, overdispersion)

Arguments

F_matrix	A matrix representing the true VAF values of a series of mutations in a set of samples (F matrix).
depth	A numeric value representing the mean depth of sequencing.
overdispersion	A numeric value representing the overdispersion parameter for the negative binomial distribution used to simulate the depth of sequencing.

Value

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

Examples

# Calculate the noisy VAF values of a series of mutations in a set of samples, given the true 
# VAF values in the F matrix F_true, a depth of 30 and an overdispersion of 5

# Simulate the noise-free F matrix of a tumor with 50 clones,
# 10 samples, k = 5, following a positive selection model
F_true <- create_instance(
  n = 50,
  m = 10,
  k = 5,
  selection = "positive", 
  noisy = FALSE)$F_true

# Then we add the noise using a depth of 30 and an overdispersion of 5.
noisy_F <- add_noise(F_true, 30, 5)

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