setEBV: Set EBV

In AlphaSimR: Breeding Program Simulations

Set EBV

Description

Adds genomic estimated values to a populations's EBV slot using output from a genomic selection functions. The genomic estimated values can be either estimated breeding values, estimated genetic values, or estimated general combining values.

Usage

setEBV(
  pop,
  solution,
  value = "gv",
  targetPop = NULL,
  append = FALSE,
  simParam = NULL
)

Arguments

pop	an object of Pop-class
solution	an object of RRsol-class
value	the genomic value to be estimated. Can be either "gv", "bv", "female", or "male".
targetPop	an optional target population that can be used when value is "bv", "female", or "male". When supplied, the allele frequency in the targetPop is used to set these values.
append	should estimated values be appended to existing data in the EBV slot. If TRUE, a new column is added. If FALSE, existing data is replaced with the new estimates.
simParam	an object of SimParam

Value

Returns an object of Pop-class

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 = RRBLUP(pop, simParam=SP)
pop = setEBV(pop, ans, simParam=SP)

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

AlphaSimR documentation built on Nov. 2, 2023, 6:01 p.m.