create_instance: Create a tumor phylogenetic tree instance

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

Create a tumor phylogenetic tree instance

Description

This function generates a tumor phylogenetic tree instance, composed by a mutation matrix (B matrix), a matrix of true variant allele frequencies (F_true), a matrix of noisy variant allele frequencies (F), and a matrix of clone frequencies in samples (U).

Usage

create_instance(
  n,
  m,
  k,
  selection,
  noisy = TRUE,
  depth = 30,
  seed = Sys.time()
)

Arguments

n	An integer representing the number of clones.
m	An integer representing the number of samples.
k	A numeric value that determines the linearity of the tree topology. Also referred to as the topology parameter. Increasing values of this parameter increase the linearity of the topology. When 'k' is set to 1, all nodes have equal probabilities of being chosen as parents, resulting in a completely random topology.
selection	A character string representing the evolutionary mode the tumor follows. This should be either "positive" or "neutral".
noisy	A logical value indicating whether to add noise to the frequency matrix. If 'TRUE', noise is added to the frequency matrix. If 'FALSE', no noise is added. 'TRUE' by default.
depth	A numeric value representing the mean depth of sequencing. 30 by default.
seed	A numeric value used to set the seed for the random number generator. Sys.time() by default.

Details

The B matrix is a square matrix representing the mutation relationships between the clones in the tumor, or, in other words, it represents the topology of the phylogenetic tree. The F_true matrix represents the true variant allele frequencies of the mutations present in the tumor in a set of samples. The F matrix represents the noisy variant allele frequencies of the mutations in the same set of samples. The U matrix represents the frequencies of the clones in the tumor in the set of samples.

Value

A list containing four elements: 'F', a matrix representing the noisy frequencies of each mutation in each sample; 'B', a matrix representing the mutation relationships between the clones in the tumor; 'U', a matrix that represents the frequencies of the clones in the tumor in the set of samples; and 'F_true', a matrix representing the true frequencies of each mutation in each sample.

Examples

# Create an instance of a tumor with 10 clones,
# 4 samples, k = 1, neutral evolution and
# added noise with depth = 500
I1 <- create_instance(
  n = 10,
  m = 4,
  k = 1,
  selection = "neutral",
  depth = 500)
  

# Create an instance of a tumor with 50 clones,
# 10 samples, k = 5, positive selection and
# added noise with depth = 500
I2 <- create_instance(
  n = 50,
  m = 10,
  k = 5,
  selection = "positive", 
  noisy = TRUE,
  depth = 500)
  
  
# Create an instance of a tumor with 100 clones,
# 25 samples, k = 0, positive selection without 
# noise
I3 <- create_instance(
  n = 100,
  m = 25,
  k = 0,
  selection = "positive", 
  noisy = FALSE)

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