creating.trait: Generation of genomic traits

In MoBPS: Modular Breeding Program Simulator

Generation of genomic traits

Description

Generation of the trait in a starting population

Usage

creating.trait(
  population,
  trait.name = NULL,
  mean.target = NULL,
  var.target = NULL,
  qtl.position.shared = FALSE,
  trait.cor = NULL,
  trait.cor.include = NULL,
  n.additive = 0,
  n.equal.additive = 0,
  n.dominant = 0,
  n.equal.dominant = 0,
  n.overdominant = 0,
  n.equal.overdominant = 0,
  n.qualitative = 0,
  n.quantitative = 0,
  effect.distribution = "gauss",
  gamma.shape1 = 1,
  gamma.shape2 = 1,
  real.bv.add = NULL,
  real.bv.mult = NULL,
  real.bv.dice = NULL,
  n.traits = 0,
  base.bv = NULL,
  new.residual.correlation = NULL,
  new.breeding.correlation = NULL,
  is.maternal = NULL,
  is.paternal = NULL,
  fixed.effects = NULL,
  trait.pool = 0,
  gxe.correlation = NULL,
  n.locations = NULL,
  gxe.max = 0.85,
  gxe.min = 0.7,
  location.name = NULL,
  gxe.combine = TRUE,
  dominant.only.positive = FALSE,
  exclude.snps = NULL,
  var.additive.l = NULL,
  var.dominant.l = NULL,
  var.overdominant.l = NULL,
  var.qualitative.l = NULL,
  var.quantitative.l = NULL,
  effect.size.equal.add = 1,
  effect.size.equal.dom = 1,
  effect.size.equal.over = 1,
  polygenic.variance = 100,
  bve.mult.factor = NULL,
  bve.poly.factor = NULL,
  set.zero = FALSE,
  bv.standard = FALSE,
  replace.traits = FALSE,
  remove.invalid.qtl = TRUE,
  randomSeed = NULL,
  verbose = TRUE,
  use.recalculate.manual = NULL,
  new.phenotype.correlation = NULL,
  shuffle.traits = NULL,
  shuffle.cor = NULL,
  bv.total = 0
)

Arguments

population	Population list
trait.name	Name of the trait generated
mean.target	Target mean
var.target	Target variance
qtl.position.shared	Set to TRUE to put QTL effects on the same markers for different traits
trait.cor	Target correlation between QTL-based traits (underlying true genomic values)
trait.cor.include	Vector of traits to be included in the modelling of correlated traits (default: all - needs to match with trait.cor)
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 dominant QTL with equal effect size
n.overdominant	Number of overdominant QTL with effect size drawn from absolute value of a gaussian distribution
n.equal.overdominant	Number of overdominant QTL with equal effect size
n.qualitative	Number of qualitative epistatic QTL
n.quantitative	Number of quantitative epistatic QTL
effect.distribution	Set to "gamma" for gamma distribution effects with gamma.shape1, gamma.shape2 instead of gaussian (default: "gauss")
gamma.shape1	Default: 1
gamma.shape2	Default: 1
real.bv.add	Single Marker effects
real.bv.mult	Two Marker effects
real.bv.dice	Multi-marker effects
n.traits	Number of traits (If more than traits via real.bv.X use traits with no directly underlying QTL)
base.bv	Average genetic value of a trait
new.residual.correlation	Correlation of the simulated enviromental variance
new.breeding.correlation	Correlation of the simulated genetic variance (child share! heritage is not influenced!
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)
fixed.effects	Matrix containing fixed effects (p x k -matrix with p being the number of traits and k being number of fixed effects; default: p x 1 matrix with 0s (additional intercept))
trait.pool	Vector providing information for which pools QTLs of this trait are activ (default: 0 - all pools)
gxe.correlation	Correlation matrix between locations / environments (default: only one location, sampled from gxe.max / gxe.min)
n.locations	Number of locations / environments to consider for the GxE model
gxe.max	Maximum correlation between locations / environments when generating correlation matrix via sampling (default: 0.85)
gxe.min	Minimum correlation between locations / environments when generating correlation matrix via sampling (default: 0.70)
location.name	Same of the different locations / environments used
gxe.combine	Set to FALSE to not view the same trait from different locations / environments as the sample trait in the prediction model (default: TRUE)
dominant.only.positive	Set to TRUE to always assign the heterozygous variant with the higher of the two homozygous effects (e.g. hybrid breeding); default: FALSE
exclude.snps	Marker were no QTL are simulated on
var.additive.l	Variance of additive QTL
var.dominant.l	Variance of dominante QTL
var.overdominant.l	Variance of overdominante 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
effect.size.equal.over	Effect size of the QTLs in n.equal.overdominant
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
set.zero	Set to TRUE to have no effect on the 0 genotype (or 00 for QTLs with 2 underlying SNPs)
bv.standard	Set TRUE to standardize trait mean and variance via bv.standardization()
replace.traits	If TRUE delete the simulated traits added before
remove.invalid.qtl	Set to FALSE to deactive the automatic removal of QTLs on markers that do not exist
randomSeed	Set random seed of the process
verbose	Set to FALSE to not display any prints
use.recalculate.manual	Set to TRUE to use recalculate.manual to calculate genomic values (all individuals and traits jointly, default: FALSE)
new.phenotype.correlation	(OLD! - use new.residual.correlation) Correlation of the simulated enviromental variance
shuffle.traits	OLD! Use trait.cor.include - Vector of traits to be included for modelling of correlated traits (default: all - needs to match with shuffle.cor)
shuffle.cor	OLD! Use trait.cor - Target Correlation between traits
bv.total	OLD! Use n.traits instead. Number of traits (If more than traits via real.bv.X use traits with no directly underlying QTL)

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. 5, 2025, 6:26 p.m.