RRBLUP_D2 {AlphaSimR} | R Documentation |
Fits an RR-BLUP model for genomic predictions that includes
dominance effects. This implementation is meant for situations where
RRBLUP_D
is too slow. Note that RRBLUP_D2
is only faster in certain situations. Most users should use
RRBLUP_D
.
RRBLUP_D2(
pop,
traits = 1,
use = "pheno",
snpChip = 1,
useQtl = FALSE,
maxIter = 10,
Va = NULL,
Vd = NULL,
Ve = NULL,
useEM = TRUE,
tol = 1e-06,
simParam = NULL,
...
)
pop |
a |
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. Only used when number of traits is greater than 1. |
Va |
marker effect variance for additive effects. If value is NULL, a reasonable starting point is chosen automatically. |
Vd |
marker effect variance for dominance effects. If value is NULL, a reasonable starting point is chosen automatically. |
Ve |
error variance. If value is NULL, a reasonable starting point is chosen automatically. |
useEM |
use EM to solve variance components. If false, the initial values are considered true. |
tol |
tolerance for EM algorithm convergence |
simParam |
an object of |
... |
additional arguments if using a function for traits |
#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=20)
#Set simulation parameters
SP = SimParam$new(founderPop)
SP$addTraitAD(10, meanDD=0.5)
SP$setVarE(h2=0.5)
SP$addSnpChip(10)
#Create population
pop = newPop(founderPop, simParam=SP)
#Run GS model and set EBV
ans = RRBLUP_D2(pop, simParam=SP)
pop = setEBV(pop, ans, simParam=SP)
#Evaluate accuracy
cor(gv(pop), ebv(pop))