Trim a pedigree to a group's ancestors — trimPedigree • nprcgenekeepr

Filters a pedigree down to the provided group (the probands) and all of their ancestors, removing unnecessary individuals from the studbook. By default only that filtering is done. Uninformative founders are removed only when removeUninformative = TRUE, and single parents are added back only when both removeUninformative and addBackParents are TRUE.

Usage

trimPedigree(
  probands,
  ped,
  removeUninformative = FALSE,
  addBackParents = FALSE
)

Arguments

probands

a character vector with the list of animals whose ancestors should be included in the final pedigree.

ped

datatable that is the Pedigree. It contains pedigree information. The fields id, sire and dam are required.

removeUninformative

logical defaults to FALSE. If set to TRUE, uninformative founders are removed.

Founders (having unknown sire and dam) that appear only one time in a pedigree are uninformative and can be removed from a pedigree without loss of information.

addBackParents

logical defaults to FALSE. If set to TRUE, the function adds back single parents to the p dataframe when one parent is known. It is ignored unless removeUninformative = TRUE. The function addBackSecondParents uses the ped dataframe, which has full complement of parents and the p dataframe, which has all uninformative parents removed to add back single parents to the p dataframe.

Value

A pedigree containing the probands and all of their ancestors. Uninformative founders are removed only when removeUninformative is TRUE, and single parents are added back only when addBackParents is also TRUE.

Examples

library(nprcgenekeepr)
examplePedigree <- nprcgenekeepr::examplePedigree
breederPed <- qcStudbook(examplePedigree,
  minSireAge = 2,
  minDamAge = 2,
  reportChanges = FALSE,
  reportErrors = FALSE
)
focalAnimals <- breederPed$id[!(is.na(breederPed$sire) &
  is.na(breederPed$dam)) &
  is.na(breederPed$exit)]
breederPed <- setPopulation(ped = breederPed, ids = focalAnimals)
trimmedPed <- trimPedigree(focalAnimals, breederPed)
trimmedPedInformative <- trimPedigree(focalAnimals, breederPed,
  removeUninformative = TRUE
)
nrow(breederPed)
#> [1] 3694
nrow(trimmedPed)
#> [1] 704
nrow(trimmedPedInformative)
#> [1] 509