sim_inf_chrom {junctions}R Documentation

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, initial_heterozygosity, total_runtime, morgan, markers, seed)

Arguments

pop_size

Population Size

initial_heterozygosity

Initial frequency of heterozygosity (e.g. in Hardy-Weinberg this equates to 2pq)

total_runtime

Maximum time after which the simulation is to be stopped

morgan

Size of the chromosome in Morgan

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]

detectedJunctions

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

Author(s)

Thijs Janzen

Examples

  N = 100 #population size
  H_0 = 0.5 #initial heterozygosity
  maxT = 1000 #run time
  C = 1 #number of recombinations per meiosis
  numMarkers = 100
  seed = 42

  v <- sim_inf_chrom(N, H_0, maxT, C, numMarkers, seed)

  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"))

[Package junctions version 1.1 Index]