RRBLUP_SCA {AlphaSimR}

RR-BLUP SCA Model

Description

An extention of RRBLUP_GCA that adds dominance effects. Note that we have not seen any consistent benefit of this model over RRBLUP_GCA.

Usage

RRBLUP_SCA(
  pop,
  traits = 1,
  use = "pheno",
  snpChip = 1,
  useQtl = FALSE,
  maxIter = 40L,
  simParam = NULL,
  ...
)

Arguments

pop

a Pop-class to serve as the training population

traits

an integer indicating the trait to model, a trait name, or a function of the traits returning a single value.

use

train model using phenotypes "pheno", genetic values "gv", estimated breeding values "ebv", breeding values "bv", or randomly "rand"

snpChip

an integer indicating which SNP chip genotype to use

useQtl

should QTL genotypes be used instead of a SNP chip. If TRUE, snpChip specifies which trait's QTL to use, and thus these QTL may not match the QTL underlying the phenotype supplied in traits.

maxIter

maximum number of iterations for convergence.

simParam

an object of SimParam

...

additional arguments if using a function for traits

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=2, nChr=1, segSites=20)

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

SP$addTraitA(10)
SP$setVarE(h2=0.5)
SP$addSnpChip(10)

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

#Run GS model and set EBV
ans = RRBLUP_SCA(pop, simParam=SP)
pop = setEBV(pop, ans, simParam=SP)

#Evaluate accuracy
cor(gv(pop), ebv(pop))