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Generate a genetic value report for a pedigree

Source: R/reportGV.R
reportGV.Rd

This is the main function for the Genetic Value Analysis.

Usage

reportGV(
  ped,
  guIter = 1000L,
  guThresh = 1L,
  pop = NULL,
  byID = TRUE,
  updateProgress = NULL,
  breedingTable = NULL,
  gestationTable = NULL,
  breedingAgeDefault = NULL,
  gestationDefault = NULL,
  kinshipOverrides = NULL
)

Arguments

ped

The pedigree information in data.frame format

guIter

Integer indicating the number of iterations for the gene-drop analysis. Default is 1000 iterations

guThresh

Integer indicating the threshold number of animals for defining a unique allele. Default considers an allele "unique" if it is found in only 1 animal.

pop

Character vector with animal IDs to consider as the population of interest. The default is NULL.

byID

Logical variable of length 1 that is passed through to eventually be used by alleleFreq(), which calculates the count of each allele in the provided vector. If byID is TRUE and ids are provided, the function will only count the unique alleles for an individual (homozygous alleles will be counted as 1).

updateProgress

Function or NULL. If this function is defined, it will be called during each iteration to update a shiny::Progress object.

breedingTable

Optional data.frame overriding the bundled per-species minimum breeding ages used by the unknown-parent mean-kinship correction. NULL (the default) uses the bundled speciesGestation table.

gestationTable

Optional data.frame overriding the bundled per-species gestation windows used by the correction's conception window. NULL uses the bundled table.

breedingAgeDefault

Optional numeric fallback minimum breeding age (years) for species absent from the table. NULL uses the built-in 2 years.

gestationDefault

Optional integer fallback gestation window (days) for species absent from the table. NULL uses the built-in 210 days.

kinshipOverrides

Optional data.frame of outside-information kinship overrides (id1, id2, kinship; the coefficient f, not relatedness r) applied to the kinship matrix before mean kinship and the unknown-parent correction. NULL (the default) leaves the pedigree-derived matrix unchanged. Ids outside the analysis set are warn-dropped (the run is not aborted). An override REFINES the named kinship cell; it does not suppress the + sexMean / 2 unknown-parent correction, which is kept for every animal missing one parent. See applyKinshipOverrides.

Value

An object of class nprcgenekeeprGV: a list with elements report (a dataframe with the genetic value report, with animals ranked in order of descending value; it carries both a gu column and a guSE column – the Monte Carlo sampling standard error of each genome uniqueness estimate, see calcGUSE), kinship (the kinship matrix), gu (a dataframe with a gu column of genome uniqueness values and a guSE column of their standard errors; gu and guSE are reported as 0 for unknown-origin both-unknown "Undetermined" animals, whose apparent uniqueness is an artifact of unknown parentage), fe (founder equivalents), fg (founder genome equivalents), fgSE (the Monte Carlo sampling standard error of fg, computed from the same gene drop; a single colony-level number, NA when a contributing founder is retained in zero gene-drop iterations – see calcFGSE), neGD (gene diversity retained in the founding gene pool, 1 - 1 / (2 * fg); a colony-level scalar beside fg, NA when fg is NA; see calcGeneDiversity), neSexRatio (the demographic sex-ratio effective size, 4 * nMale * nFemale / (nMale + nFemale), over the current living breeders – a different population than fg and neGD; 0 when a breeding sex is absent; see calcNeSexRatio), neVariance (the variance effective size, the mean-adjusted Crow-Kimura form (N * kbar - 1) / (kbar - 1 + Vk / kbar) over the same current living breeders; NA when fewer than two living breeders; see calcNeVariance), maleFounders and femaleFounders (dataframes of the known male and female founder records), nMaleFounders and nFemaleFounders (the counts of those founders), and total (the total number of known founders).

Details

Reported genome uniqueness (gu) is set to 0 for "Undetermined" animals – those with both parents unknown (U-id aware) and no recorded origin – because their apparent uniqueness is an artifact of unknown parentage (decline-to-credit policy). Imports (both parents unknown but with a recorded origin) and all other animals are unaffected, and calcGU itself is unchanged.

Examples

library(nprcgenekeepr)
examplePedigree <- nprcgenekeepr::examplePedigree
breederPed <- qcStudbook(examplePedigree,
  minParentAge = 2,
  reportChanges = FALSE,
  reportErrors = FALSE
)
focalAnimals <- breederPed$id[!(is.na(breederPed$sire) &
  is.na(breederPed$dam)) &
  is.na(breederPed$exit)]
ped <- setPopulation(ped = breederPed, ids = focalAnimals)
trimmedPed <- trimPedigree(focalAnimals, breederPed)
probands <- ped$id[ped$population]
ped <- trimPedigree(probands, ped,
  removeUninformative = FALSE,
  addBackParents = FALSE
)
geneticValue <- reportGV(ped,
  guIter = 50, # should be >= 1000
  guThresh = 3,
  byID = TRUE,
  updateProgress = NULL
)
trimmedGeneticValue <- reportGV(trimmedPed,
  guIter = 50, # should be >= 1000
  guThresh = 3,
  byID = TRUE,
  updateProgress = NULL
)
rpt <- trimmedGeneticValue[["report"]]
kmat <- trimmedGeneticValue[["kinship"]]
f <- trimmedGeneticValue[["total"]]
mf <- trimmedGeneticValue[["maleFounders"]]
ff <- trimmedGeneticValue[["femaleFounders"]]
nmf <- trimmedGeneticValue[["nMaleFounders"]]
nff <- trimmedGeneticValue[["nFemaleFounders"]]
fe <- trimmedGeneticValue[["fe"]]
fg <- trimmedGeneticValue[["fg"]]