genParam: Sumarize genetic parameters

In AlphaSimR: Breeding Program Simulations

Sumarize genetic parameters

Description

Calculates genetic and genic additive and dominance variances for an object of Pop-class

Usage

genParam(pop, simParam = NULL)

Arguments

pop	an object of Pop-class
simParam	an object of SimParam

Value

varA

an nTrait by nTrait matrix of additive genetic variances

varD

an nTrait by nTrait matrix of dominance genetic variances

varAA

an nTrait by nTrait matrix of additive-by-additive genetic variances

varG

an nTrait by nTrait matrix of total genetic variances

genicVarA

an nTrait vector of additive genic variances

genicVarD

an nTrait vector of dominance genic variances

genicVarAA

an nTrait vector of additive-by-additive genic variances

genicVarG

an nTrait vector of total genic variances

covA_HW

an nTrait vector of additive covariances due to non-random mating

covD_HW

an nTrait vector of dominance covariances due to non-random mating

covAA_HW

an nTrait vector of additive-by-additive covariances due to non-random mating

covG_HW

an nTrait vector of total genic covariances due to non-random mating

covA_L

an nTrait vector of additive covariances due to linkage disequilibrium

covD_L

an nTrait vector of dominance covariances due to linkage disequilibrium

covAA_L

an nTrait vector of additive-by-additive covariances due to linkage disequilibrium

covAD_L

an nTrait vector of additive by dominance covariances due to linkage disequilibrium

covAAA_L

an nTrait vector of additive by additive-by-additive covariances due to linkage disequilibrium

covDAA_L

an nTrait vector of dominance by additive-by-additive covariances due to linkage disequilibrium

covG_L

an nTrait vector of total genic covariances due to linkage disequilibrium

mu

an nTrait vector of trait means

mu_HW

an nTrait vector of expected trait means under random mating

gv

a matrix of genetic values with dimensions nInd by nTraits

bv

a matrix of breeding values with dimensions nInd by nTraits

dd

a matrix of dominance deviations with dimensions nInd by nTraits

aa

a matrix of additive-by-additive epistatic deviations with dimensions nInd by nTraits

gv_mu

an nTrait vector of intercepts with dimensions nInd by nTraits

gv_a

a matrix of additive genetic values with dimensions nInd by nTraits

gv_d

a matrix of dominance genetic values with dimensions nInd by nTraits

gv_aa

a matrix of additive-by-additive genetic values with dimensions nInd by nTraits

alpha

a list of average allele subsitution effects with length nTraits

alpha_HW

a list of average allele subsitution effects at Hardy-Weinberg equilibrium with length nTraits

Examples

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

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$addTraitAD(10, meanDD=0.5)
SP$setVarE(h2=0.5)


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

AlphaSimR documentation built on Nov. 1, 2024, 5:07 p.m.