Calculate founder equivalents and founder genome equivalents

Part of the Genetic Value Analysis

Usage

calcFEFG(ped, alleles)

Arguments

ped

the pedigree information in datatable format. Pedigree (req. fields: id, sire, dam, gen, population).

The pedigree must have no partial parentage (every animal has both parents known or both unknown); calcFEFG stops with an error otherwise.

alleles

dataframe contains an AlleleTable. This is a table of allele information produced by geneDrop().

Value

The list containing the founder equivalents, FE = 1 / sum(p ^ 2), and the founder genome equivalents, FG = 1 / sum( (p ^ 2) / r) where p is the vector of founder mean contributions to the current descendants and r is the mean number of founder alleles retained in the gene dropping experiment.

FE is deterministic and always returned. FG is NA (with a warning) when a contributing founder (p > 0) is retained in zero of the gene-drop iterations (r == 0), which would otherwise collapse FG silently to 0; raise the number of iterations. See calcFGSE for the sampling standard error of FG.

Examples

data(lacy1989Ped)
## Example from Analysis of Founder Representation in Pedigrees: Founder
## Equivalents and Founder Genome Equivalents.
## Zoo Biology 8:111-123, (1989) by Robert C. Lacy

library(nprcgenekeepr)
ped <- nprcgenekeepr::lacy1989Ped
alleles <- lacy1989PedAlleles
pedFactors <- data.frame(
  id = as.factor(ped$id),
  sire = as.factor(ped$sire),
  dam = as.factor(ped$dam),
  gen = ped$gen,
  population = ped$population,
  stringsAsFactors = TRUE
)
allelesFactors <- geneDrop(pedFactors$id, pedFactors$sire, pedFactors$dam,
  pedFactors$gen,
  genotype = NULL, n = 1000,
  updateProgress = NULL
)
feFg <- calcFEFG(ped, alleles)
feFgFactors <- calcFEFG(pedFactors, allelesFactors)