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

simulate_sequence

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_sequence(
  input_data = NA,
  pop_size = NA,
  initial_frequencies = NA,
  total_runtime = 100,
  morgan = 1,
  recombination_rate = NA,
  num_threads = 1,
  select_matrix = NA,
  markers = NA,
  verbose = FALSE,
  multiplicative_selection = TRUE,
  mutation_rate = 0,
  substitution_matrix = matrix(1/4, 4, 4)
)

Arguments

`input_data`	Genomic data used as input, should be of type genomeadmixr_data. Either a single dataset is provided, or a list of multiple genomeadmixr_data objects.
`pop_size`	Vector containing the number of individuals in both populations.
`initial_frequencies`	A vector describing the initial contribution of each provided input data set to the starting hybrid swarm. 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)
`recombination_rate`	rate in cM / Mbp, used to map recombination to the markers. If the recombination_rate is not set, the value for Morgan is used, assuming that the markers included span an entire chromosome.
`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, these markers are tracked for every generation.
`verbose`	Verbose output if TRUE. Default value is FALSE
`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.
`mutation_rate`	the per base probability of mutation. Default is 0.
`substitution_matrix`	a 4x4 matrix representing the probability of mutating to another base (where [1/2/3/4] = [a/c/t/g]), conditional on the event of a mutation happening. Default is the JC69 matrix, with equal probabilities for all transitions / transversions.

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.