sim_backcrossing: Function to simulate data using a back crossing scheme

In thijsjanzen/junctions: The Breakdown of Genomic Ancestry Blocks in Hybrid Lineages

Function to simulate data using a back crossing scheme

Description

Individual based simulation of the accumulation of junctions, under a back crossing scheme

Usage

sim_backcrossing(
  population_size = 100,
  freq_ancestor_1 = 0.5,
  total_runtime = 5,
  size_in_morgan = 1,
  number_of_markers = 100,
  seed = 6,
  time_points = -1
)

Arguments

population_size	Population size
freq_ancestor_1	Frequency of ancestor 1 at t = 0
total_runtime	Number of generations to simulate
size_in_morgan	Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
number_of_markers	number of molecular markers
seed	Seed of the pseudo-random number generator
time_points	vector with time points at which local ancestry has to be recorded to be returned at the end of the simulation. If left at -1, ancestry is recorded at every generation (computationally heavy).

Value

List with five entries: average_junctions: average number of junctions over time, detected_junctions: average number of detected junctions, given the markers. markers: vector with the locations of the molecular markers, junction_distribution: distribution of junctions per time step average_heterozygosity: average heterozygosity.

Examples

sim_backcrossing(population_size = 100,
                       total_runtime = 5,
                       size_in_morgan = 1, number_of_markers = 100, seed = 6,
                       time_points = 1:5)

thijsjanzen/junctions documentation built on Feb. 16, 2024, 12:14 p.m.