RR-BLUP SCA Model — RRBLUP

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))
#>        est_GV_Trait1
#> Trait1            NA