sim_phased_unphased: Individual Based Simulation of the accumulation of junctions

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

Individual Based Simulation of the accumulation of junctions

Description

Individual based simulation of the accumulation of junctions, returning phased and unphased data. Ancestry on both chromosomes of 10 randomly sampled individuals per generations is returned.

Usage

sim_phased_unphased(
  pop_size = 100,
  freq_ancestor_1 = 0.5,
  total_runtime = 100,
  size_in_morgan = 1,
  markers = 100,
  time_points = -1,
  num_threads = 1,
  verbose = FALSE,
  record_true_junctions = FALSE,
  num_indiv_sampled = 10,
  coverage = 1,
  error_rate = 0
)

Arguments

pop_size	Population Size
freq_ancestor_1	Frequency of ancestor 1 at t = 0
total_runtime	Maximum time after which the simulation is to be stopped
size_in_morgan	Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
markers	If a single number is provided, the number is used as the total number of markers generated either randomly, or using a regular distribution (a regular distribution is chosen if the number is negative). If a vector is provided, that vector is used.
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).
num_threads	default is 1. -1 takes all available threads.
verbose	displays a progress bar
record_true_junctions	keep track of the true number of junctions?
num_indiv_sampled	the number of individuals sampled at each time point to be genotyped
coverage	fraction of markers that can be succesfully phased
error_rate	fraction of markers that are erroneously phased (e.g. swapped)

Value

a tibble with five columns: [time, individual, marker location, ancestry chromosome 1, ancestry chromosome 2]

Examples

## Not run: 
sim_phased_unphased(pop_size = 100, freq_ancestor_1 = 0.5,
                    total_runtime = 10, size_in_morgan = 1,
                    markers = 10, time_points = c(0, 5, 10),
                    num_threads = 1)

## End(Not run)

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