Calculates 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).

It is assumed that the pedigree has no partial parentage

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 average number of descendants and r is the mean number of founder alleles retained in the gene dropping experiment.

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 = 5000,
                           updateProgress = NULL)
feFg <- calcFEFG(ped, alleles)
feFgFactors <- calcFEFG(pedFactors, allelesFactors)