creating.trait: Generation of genomic traits

In MoBPS: Modular Breeding Program Simulator

Description

Generation of the trait in a starting population

Usage

creating.trait(
  population,
  real.bv.add = NULL,
  real.bv.mult = NULL,
  real.bv.dice = NULL,
  bv.total = 0,
  polygenic.variance = 100,
  bve.mult.factor = NULL,
  bve.poly.factor = NULL,
  base.bv = NULL,
  new.phenotype.correlation = NULL,
  new.residual.correlation = NULL,
  new.breeding.correlation = NULL,
  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,
  randomSeed = NULL,
  shuffle.traits = NULL,
  shuffle.cor = NULL,
  replace.traits = FALSE,
  trait.name = NULL,
  remove.invalid.qtl = TRUE,
  bv.standard = FALSE,
  mean.target = NULL,
  var.target = NULL,
  verbose = TRUE,
  is.maternal = NULL,
  is.paternal = NULL
)

Arguments

population	Population list
real.bv.add	Single Marker effects
real.bv.mult	Two Marker effects
real.bv.dice	Multi-marker effects
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
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!
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
randomSeed	Set random seed of the process
shuffle.traits	Combine different traits into a joined trait
shuffle.cor	Target Correlation between shuffeled traits
replace.traits	If TRUE delete the simulated traits added before
trait.name	Name of the trait generated
remove.invalid.qtl	Set to FALSE to deactive the automatic removal of QTLs on markers that do not exist
bv.standard	Set TRUE to standardize trait mean and variance via bv.standardization()
mean.target	Target mean
var.target	Target variance
verbose	Set to FALSE to not display any prints
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)

Value

Population-list with one or more additional new traits

Examples

population <- creating.diploid(nsnp=1000, nindi=100)
population <- creating.trait(population, n.additive=100)

MoBPS documentation built on Nov. 9, 2021, 5:08 p.m.