founder.simulation {MoBPS}

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,
  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
)

Arguments

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)

Examples

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