creating.diploid: Generation of the starting population
In MoBPS: Modular Breeding Program Simulator

Description Usage Arguments Value Examples

Generation of the starting population

creating.diploid(
  dataset = NULL,
  vcf = NULL,
  chr.nr = NULL,
  bp = NULL,
  snp.name = NULL,
  hom0 = NULL,
  hom1 = NULL,
  bpcm.conversion = 0,
  nsnp = 0,
  nindi = 0,
  freq = "beta",
  population = NULL,
  sex.s = "fixed",
  add.chromosome = FALSE,
  generation = 1,
  class = 0L,
  sex.quota = 0.5,
  chromosome.length = NULL,
  length.before = 5,
  length.behind = 5,
  real.bv.add = NULL,
  real.bv.mult = NULL,
  real.bv.dice = NULL,
  snps.equidistant = NULL,
  change.order = FALSE,
  bv.total = 0,
  polygenic.variance = 100,
  bve.mult.factor = NULL,
  bve.poly.factor = NULL,
  base.bv = NULL,
  add.chromosome.ends = TRUE,
  new.phenotype.correlation = NULL,
  new.residual.correlation = NULL,
  new.breeding.correlation = NULL,
  add.architecture = NULL,
  snp.position = NULL,
  position.scaling = FALSE,
  bit.storing = FALSE,
  nbits = 30,
  randomSeed = NULL,
  miraculix = TRUE,
  miraculix.dataset = TRUE,
  n.additive = 0,
  n.equal.additive = 0,
  n.dominant = 0,
  n.equal.dominant = 0,
  n.qualitative = 0,
  n.quantitative = 0,
  dominant.only.positive = FALSE,
  var.additive.l = NULL,
  var.dominant.l = NULL,
  var.qualitative.l = NULL,
  var.quantitative.l = NULL,
  effect.size.equal.add = 1,
  effect.size.equal.dom = 1,
  exclude.snps = NULL,
  replace.real.bv = FALSE,
  shuffle.traits = NULL,
  shuffle.cor = NULL,
  skip.rest = FALSE,
  enter.bv = TRUE,
  name.cohort = NULL,
  template.chip = NULL,
  beta.shape1 = 1,
  beta.shape2 = 1,
  time.point = 0,
  creating.type = 0,
  trait.name = NULL,
  share.genotyped = 1,
  genotyped.s = NULL,
  map = NULL,
  remove.invalid.qtl = TRUE,
  verbose = TRUE,
  bv.standard = FALSE,
  mean.target = NULL,
  var.target = NULL,
  is.maternal = NULL,
  is.paternal = NULL,
  vcf.maxsnp = Inf,
  internal = FALSE
)

`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)
`nsnp`	number of markers to generate in a random dataset
`nindi`	number of inidividuals to generate in a random dataset
`freq`	frequency of allele 1 when randomly generating a dataset
`population`	Population list
`sex.s`	Specify which newly added individuals are male (1) or female (2)
`add.chromosome`	If TRUE add an additional chromosome to the dataset
`generation`	Generation of the newly added individuals (default: 1)
`class`	Migration level of the newly added individuals
`sex.quota`	Share of newly added female individuals (deterministic if sex.s="fixed", alt: sex.s="random")
`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)
`real.bv.add`	Single Marker effects
`real.bv.mult`	Two Marker effects
`real.bv.dice`	Multi-marker effects
`snps.equidistant`	Use equidistant markers (computationally faster! ; default: TRUE)
`change.order`	If TRUE sort markers according to given marker positions
`bv.total`	Number of traits (If more than traits via real.bv.X use traits with no directly underlying QTL)
`polygenic.variance`	Genetic variance of traits with no underlying QTL
`bve.mult.factor`	Multiplicate trait value times this
`bve.poly.factor`	Potency trait value over this
`base.bv`	Average genetic value of a trait
`add.chromosome.ends`	Add chromosome ends as recombination points
`new.phenotype.correlation`	(OLD! - use new.residual.correlation) Correlation of the simulated enviromental variance
`new.residual.correlation`	Correlation of the simulated enviromental variance
`new.breeding.correlation`	Correlation of the simulated genetic variance (child share! heritage is not influenced!
`add.architecture`	Add genetic architecture (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
`n.additive`	Number of additive QTL with effect size drawn from a gaussian distribution
`n.equal.additive`	Number of additive QTL with equal effect size (effect.size)
`n.dominant`	Number of dominant QTL with effect size drawn from a gaussian distribution
`n.equal.dominant`	Number of n.equal.dominant QTL with equal effect size
`n.qualitative`	Number of qualitative epistatic QTL
`n.quantitative`	Number of quantitative epistatic QTL
`dominant.only.positive`	Set to TRUE to always asign the heterozygous variant with the higher of the two homozygous effects (e.g. hybrid breeding); default: FALSE
`var.additive.l`	Variance of additive QTL
`var.dominant.l`	Variance of dominante QTL
`var.qualitative.l`	Variance of qualitative epistatic QTL
`var.quantitative.l`	Variance of quantitative epistatic QTL
`effect.size.equal.add`	Effect size of the QTLs in n.equal.additive
`effect.size.equal.dom`	Effect size of the QTLs in n.equal.dominant
`exclude.snps`	Marker were no QTL are simulated on
`replace.real.bv`	If TRUE delete the simulated traits added before
`shuffle.traits`	Combine different traits into a joined trait
`shuffle.cor`	Target Correlation between shuffeled traits
`skip.rest`	Internal variable needed when adding multipe chromosomes jointly
`enter.bv`	Internal parameter
`name.cohort`	Name of the newly added cohort
`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
`time.point`	Time point at which the new individuals are generated
`creating.type`	Technique to generate new individuals (usage in web-based application)
`trait.name`	Name of the trait generated
`share.genotyped`	Share of individuals genotyped in the founders
`genotyped.s`	Specify with newly added individuals are genotyped (1) or not (0)
`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()
`remove.invalid.qtl`	Set to FALSE to deactive the automatic removal of QTLs on markers that do not exist
`verbose`	Set to FALSE to not display any prints
`bv.standard`	Set TRUE to standardize trait mean and variance via bv.standardization() - automatically set to TRUE when mean/var.target are used
`mean.target`	Target mean
`var.target`	Target variance
`is.maternal`	Vector coding if a trait is caused by a maternal effect (Default: all FALSE)
`is.paternal`	Vector coding if a trait is caused by a paternal effect (Default: all FALSE)
`vcf.maxsnp`	Maximum number of SNPs to include in the genotype file (default: Inf)
`internal`	Dont touch!