fastRRBLUP {AlphaSimR} | R Documentation |
Fast RR-BLUP
Description
Solves an RR-BLUP model for genomic predictions given known variance
components. This implementation is meant as a fast and low memory
alternative to RRBLUP
or RRBLUP2
. Unlike
the those functions, the fastRRBLUP does not fit fixed effects (other
than the intercept) or account for unequal replication.
Usage
fastRRBLUP(
pop,
traits = 1,
use = "pheno",
snpChip = 1,
useQtl = FALSE,
maxIter = 1000,
Vu = NULL,
Ve = NULL,
simParam = NULL,
...
)
Arguments
pop |
a |
traits |
an integer indicating the trait to model, a trait name, or a function of the traits returning a single value. Only univariate models are supported. |
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. |
Vu |
marker effect variance. If value is NULL, a reasonable value is chosen automatically. |
Ve |
error variance. If value is NULL, a reasonable value is chosen automatically. |
simParam |
an object of |
... |
additional arguments if using a function for traits |
Examples
#Create founder haplotypes
founderPop = quickHaplo(nInd=10, 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 = fastRRBLUP(pop, simParam=SP)
pop = setEBV(pop, ans, simParam=SP)
#Evaluate accuracy
cor(gv(pop), ebv(pop))