simulate_sequence {GenomeAdmixR} | R Documentation |
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.
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)
)
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:
|
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. |
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.