Add back second parents to a trimmed pedigree — addBackSecondParents • nprcgenekeepr

Uses the ped dataframe, which has full complement of parents and the uPed dataframe, which has all uninformative parents removed to add back single parents to the uPed dataframe where one parent is known. The parents are added back to the pedigree as an ID record with NA for both sire and dam of the added back ID.

Usage

addBackSecondParents(uPed, ped)

Arguments

uPed: a trimmed pedigree dataframe with uninformative founders removed.
ped: the full (untrimmed) pedigree dataframe, from which the second parents are taken.

Value

A pedigree with single parents added. It is a data.table once any record is added and a plain dataframe when none is.

Examples

examplePedigree <- nprcgenekeepr::examplePedigree
breederPed <- qcStudbook(examplePedigree,
  minSireAge = 2, minDamAge = 2,
  reportChanges = FALSE,
  reportErrors = FALSE
)
probands <- breederPed$id[!(is.na(breederPed$sire) &
  is.na(breederPed$dam)) &
  is.na(breederPed$exit)]
ped <- getProbandPedigree(probands, breederPed)
nrow(ped)
#> [1] 704
p <- removeUninformativeFounders(ped)
nrow(p)
#> [1] 509
p <- addBackSecondParents(p, ped)
nrow(p)
#> [1] 690