founder.simulation: Founder simulation

In MoBPS: Modular Breeding Program Simulator

Founder simulation

Description

Function to generate founder genotypes

Usage

founder.simulation(
  nindi = 100,
  sex.quota = 0.5,
  nsnp = 0,
  n.gen = 100,
  nfinal = NULL,
  sex.quota.final = NULL,
  big.output = FALSE,
  plot = TRUE,
  display.progress = TRUE,
  depth.pedigree = 7,
  dataset = NULL,
  vcf = NULL,
  chr.nr = NULL,
  bp = NULL,
  snp.name = NULL,
  hom0 = NULL,
  hom1 = NULL,
  bpcm.conversion = 0,
  freq = "beta",
  sex.s = "fixed",
  chromosome.length = NULL,
  length.before = 5,
  length.behind = 5,
  snps.equidistant = NULL,
  snp.position = NULL,
  position.scaling = FALSE,
  bit.storing = FALSE,
  nbits = 30,
  randomSeed = NULL,
  miraculix = TRUE,
  miraculix.dataset = TRUE,
  template.chip = NULL,
  beta.shape1 = 1,
  beta.shape2 = 1,
  map = NULL,
  verbose = TRUE,
  vcf.maxsnp = Inf,
  plot.ld = TRUE,
  plot.allele.freq = TRUE,
  xlim = NULL,
  ylim = NULL,
  nclass = 20,
  ylim.af = NULL,
  mutation.rate = 10^-8,
  remutation.rate = 10^-8,
  estimate.ne = TRUE,
  estimate.ld = TRUE
)

Arguments

nindi	number of individuals to generate in a random dataset
sex.quota	Share of newly added female individuals (deterministic if sex.s="fixed", alt: sex.s="random")
nsnp	number of markers to generate in a random dataset
n.gen	Number of generations to simulate (default: 100)
nfinal	Number of final individuals to include (default: nindi)
sex.quota.final	Share of female individuals in the final generation
big.output	Set to TRUE to export map, population list and pedigree relationship
plot	Set to FALSE to not generate LD-decay plot and allele frequency spectrum
display.progress	Set FALSE to not display progress bars. Setting verbose to FALSE will automatically deactive progress bars
depth.pedigree	Depth of the pedigree in generations (default: 7)
dataset	SNP dataset, use "random", "allhetero" "all0" when generating a dataset via nsnp,nindi
vcf	Path to a vcf-file used as input genotypes (correct haplotype phase is assumed!)
chr.nr	Vector containing the associated chromosome for each marker (default: all on the same)
bp	Vector containing the physical position (bp) for each marker (default: 1,2,3...)
snp.name	Vector containing the name of each marker (default ChrXSNPY - XY chosen accordingly)
hom0	Vector containing the first allelic variant in each marker (default: 0)
hom1	Vector containing the second allelic variant in each marker (default: 1)
bpcm.conversion	Convert physical position (bp) into a cM position (default: 0 - not done)
freq	frequency of allele 1 when randomly generating a dataset
sex.s	Specify which newly added individuals are male (1) or female (2)
chromosome.length	Length of the newly added chromosome (default: 5)
length.before	Length before the first SNP of the dataset (default: 5)
length.behind	Length after the last SNP of the dataset (default: 5)
snps.equidistant	Use equidistant markers (computationally faster! ; default: TRUE)
snp.position	Location of each marker on the genetic map
position.scaling	Manual scaling of snp.position
bit.storing	Set to TRUE if the MoBPS (not-miraculix! bit-storing is used)
nbits	Bits available in MoBPS-bit-storing
randomSeed	Set random seed of the process
miraculix	If TRUE use miraculix package for data storage, computations and dataset generation
miraculix.dataset	Set FALSE to deactive miraculix package for dataset generation
template.chip	Import genetic map and chip from a species ("cattle", "chicken", "pig")
beta.shape1	First parameter of the beta distribution for simulating allele frequencies
beta.shape2	Second parameter of the beta distribution for simulating allele frequencies
map	map-file that contains up to 5 colums (Chromsome, SNP-id, M-position, Bp-position, allele freq - Everything not provides it set to NA). A map can be imported via MoBPSmaps::ensembl.map()
verbose	Set to FALSE to not display any prints
vcf.maxsnp	Maximum number of SNPs to include in the genotype file (default: Inf)
plot.ld	Set FALSE to not generate the LD plot (default; TRUE)
plot.allele.freq	Set FALSE to not generate the allele frequency spectrum plot (default: TRUE)
xlim	Axis limits for the x-axis in the LD plot (default: NULL)
ylim	Axis limits for the y-axis in the LD plot (default: NULL)
nclass	Number of classes to consider in the allele frequency spectrum plot (default: 20)
ylim.af	Axis limits for the allele frequency spectrum plot (default: NULL)
mutation.rate	Mutation rate in each marker (default: 10^-8)
remutation.rate	Remutation rate in each marker (default: 10^-8)
estimate.ne	Set to FALSE to not estimate the effective population size (default: TRUE)
estimate.ld	Set to FALSE to not estimate the ld decay (default: TRUE)

Examples

population <- founder.simulation(nindi=100, nsnp=1000, n.gen=5)

MoBPS documentation built on Nov. 5, 2025, 6:26 p.m.