sim_inf_chrom: Individual Based Simulation of the accumulation of junctions

In 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 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

cat("example sim inf chrom")
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"))

junctions documentation built on May 29, 2024, 6:26 a.m.