setPhenoGCA: Set GCA as phenotype

In AlphaSimR: Breeding Program Simulations

Set GCA as phenotype

Description

Calculates general combining ability from a set of testers and returns these values as phenotypes for a population.

Usage

setPhenoGCA(
  pop,
  testers,
  use = "pheno",
  h2 = NULL,
  H2 = NULL,
  varE = NULL,
  corE = NULL,
  reps = 1,
  fixEff = 1L,
  p = NULL,
  inbred = FALSE,
  onlyPheno = FALSE,
  simParam = NULL
)

Arguments

pop	an object of Pop-class
testers	an object of Pop-class
use	true genetic value (gv) or phenotypes (pheno, default)
h2	a vector of desired narrow-sense heritabilities for each trait. See details in setPheno.
H2	a vector of desired broad-sense heritabilities for each trait. See details in setPheno.
varE	error (co)variances for traits. See details in setPheno.
corE	an optional matrix for correlations between errors. See details in setPheno.
reps	number of replications for phenotype. See details in setPheno.
fixEff	fixed effect to assign to the population. Used by genomic selection models only.
p	the p-value for the environmental covariate used by GxE traits. If NULL, a value is sampled at random.
inbred	are both pop and testers fully inbred. They are only fully inbred if created by newPop using inbred founders or by the makeDH function
onlyPheno	should only the phenotype be returned, see return
simParam	an object of SimParam

Value

Returns an object of Pop-class or a matrix if onlyPheno=TRUE

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10, inbred=TRUE)

#Set simulation parameters
SP = SimParam$new(founderPop)

SP$addTraitA(10)

#Create population
pop = newPop(founderPop, simParam=SP)

#Set phenotype to average per
pop2 = setPhenoGCA(pop, pop, use="gv", inbred=TRUE, simParam=SP)

AlphaSimR documentation built on Nov. 2, 2023, 6:01 p.m.