Trim pedigree to ancestors of provided group by removing uninformative individuals

Filters a pedigree down to only the ancestors of the provided group, removing unnecessary individuals from the studbook. This version builds the pedigree back in time starting from a group of probands, then moves back down the tree trimming off uninformative ancestors.

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 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. 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 that has been trimmed, had uninformative founders removed and single parents added back.

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)]
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