simulate_ancestry: Individual based simulation of the breakdown of contiguous...
In thijsjanzen/GenomeAdmixR: Simulate Admixture of Genomes

simulate_ancestry

R Documentation

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_ancestry(
  input_population = NA,
  pop_size = NA,
  number_of_founders = 2,
  initial_frequencies = NA,
  total_runtime = 100,
  morgan = 1,
  num_threads = 1,
  select_matrix = NA,
  markers = NA,
  verbose = FALSE,
  track_junctions = FALSE,
  multiplicative_selection = TRUE
)

Arguments

`input_population`	Potential earlier simulated population used as starting point for the simulation. If not provided by the user, the simulation starts from scratch.
`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.
`number_of_founders`	Number of unique ancestors
`initial_frequencies`	A vector describing the initial frequency of each ancestor. By default, equal frequencies are assumed. If a vector not summing to 1 is provided, the vector is normalized.
`total_runtime`	Number of generations
`morgan`	Length of the chromosome in Morgan (e.g. the number of crossovers during meiosis)
`num_threads`	number of threads. Default is 1. Set to -1 to use all available threads
`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`
`markers`	A vector of locations of markers (relative locations in [0, 1]). If a vector is provided, ancestry at these marker positions is tracked for every generation.
`verbose`	Verbose output if TRUE. Default value is FALSE
`track_junctions`	Track the average number of junctions over time if TRUE
`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.

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.