junctions (version 2.1.3)

sim_inf_chrom: Individual Based Simulation of the accumulation of junctions

Description

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
)

Value

avgJunctions

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

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

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"))