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Calculate founder equivalents and founder genome equivalents

Source: R/calcFEFG.R
calcFEFG.Rd

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.

Every animal with both parents unknown is treated as a separate, unrelated founder, including an animal whose id was generated to stand in for an unknown parent. Such a placeholder may in fact be a known founder, another animal in the population, or an animal outside it, so the unrelated-founder assumption can overstate FE and FG when placeholders are common. reportGV lists only the known founders, so its founder counts can be smaller than the founder set used here.

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.

References

Lacy RC. 1989. Analysis of founder representation in pedigrees: founder equivalents and founder genome equivalents. Zoo Biol 8:111-123.

See also

Other genetic value analysis: calcA(), calcFE(), calcFG(), calcFGSE(), calcGU(), calcGUSE(), calcGeneDiversity(), calcKurtosis(), calcNeSexRatio(), calcNeVariance(), calcRetention(), calcSkewness()

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)