founder.simulation: Founder simulation
In MoBPS: Modular Breeding Program Simulator

Function to generate founder genotypes

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,
  change.order = FALSE,
  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
)

`nindi`	number of inidividuals 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 assosiated 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)
`change.order`	If TRUE sort markers according to given marker positions
`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)