simulate_admixture: Individual based simulation of the breakdown of contiguous...

In thijsjanzen/GenomeAdmixR: Simulate Admixture of Genomes

Individual based simulation of the breakdown of contiguous ancestry blocks.

Description

Individual based simulation of the breakdown of contiguous ancestry blocks, with or without selection. Simulations can be started from scratch, or from a predefined input population.

Usage

simulate_admixture(
  module = ancestry_module(),
  pop_size = 100,
  total_runtime = 100,
  migration = migration_settings(),
  select_matrix = NA,
  multiplicative_selection = TRUE,
  verbose = FALSE,
  num_threads = 1
)

Arguments

module	Chosen module to simulate, either created with module_ancestry or module_sequence.
pop_size	The number of individuals in the population. If the number is larger than the number of individuals in the input population (if provided), additional individuals are sampled randomly from the input population to reach the intended size.
total_runtime	Number of generations
migration	settings associated with migration, should be created with migration_settings
select_matrix	Selection matrix indicating the markers which are under selection. If not provided by the user, the simulation proceeds neutrally. If provided, each row in the matrix should contain five entries: location location of the marker under selection (in Morgan) fitness of wildtype (aa) fitness of heterozygote (aA) fitness of homozygote mutant (AA) Ancestral type that represents the mutant allele A
multiplicative_selection	Default: TRUE. If TRUE, fitness is calculated for multiple markers by multiplying fitness values for each marker. If FALSE, fitness is calculated by adding fitness values for each marker.
verbose	Verbose output if TRUE. Default value is FALSE
num_threads	number of threads. Default is 1. Set to -1 to use all available threads

Value

A list with: population a population object, and three tibbles with allele frequencies (only contain values of a vector was provided to the argument markers: frequencies , initial_frequencies and final_frequencies. Each tibble contains four columns, time, location, ancestor and frequency, which indicates the number of generations, the location along the chromosome of the marker, the ancestral allele at that location in that generation, and finally, the frequency of that allele.

Examples

# local ancestry simulation
two_populations <- simulate_admixture(
                         module = ancestry_module(number_of_founders = 3,
                                                  morgan = 0.8),
                         migration = migration_settings(
                                         migration_rate = 0.01,
                                         population_size = c(100, 100)),
                         total_runtime = 10)
 # sequence simulation
 data(dgrp2.3R.5k.data)

sequence_population <-
      simulate_admixture(
                  module = sequence_module(molecular_data = dgrp2.3R.5k.data,
                           recombination_rate = 0.2,
                           mutation_rate = 1e-5),
                  pop_size = 1000,
                  total_runtime = 10)

thijsjanzen/GenomeAdmixR documentation built on Feb. 16, 2024, 7:27 p.m.