Individual Based Simulation of the accumulation of junctions

Individual based simulation of the accumulation of junctions for a chromosome with an infinite number of recombination sites.

Usage

sim_inf_chrom(
  pop_size = 100,
  freq_ancestor_1 = 0.5,
  total_runtime = 100,
  morgan = 1,
  markers = -1,
  seed = 42
)

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
morgan: Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
markers: The number of genetic markers superimposed on the chromosome. If markers is set to -1, no markers are superimposed (faster simulation)
seed: Seed of the pseudo-random number generator

Value

avgJunctions: vector of the average number of junctions at time = [0, total_runtime]

Examples

v <- sim_inf_chrom(pop_size = 100, freq_ancestor_1 = 0.5,
                   total_runtime = 10, morgan = 1, markers = 100,
                   seed = 42)
plot(v$avgJunctions, type = "l", xlab = "Generations",
ylab = "Number of Junctions", main = "Example Infinite Chromosome")
lines(v$detectedJunctions, col = "blue")
legend("bottomright", c("Real number","Number detected"),
       lty = 1, col = c("black", "blue"))