Add parents

Pedigree curation function Given a pedigree, find any IDs listed in the "sire" or "dam" columns that lack their own line entry and generate one.

Usage

addParents(ped)

Arguments

ped

datatable that is the Pedigree. It contains pedigree information including the IDs listed in candidates.

Value

An updated pedigree with entries added as necessary. Entries have the id and sex specified; all remaining columns are filled with NA.

Details

This must be run after to addUIds since the IDs made there are used by addParents

Examples

pedTwo <- data.frame(
  id = c("d1", "s2", "d2", "o1", "o2", "o3", "o4"),
  sire = c(NA, NA, NA, "s1", "s1", "s2", "s2"),
  dam = c(NA, NA, NA, "d1", "d2", "d2", "d2"),
  sex = c("F", "M", "F", "F", "F", "F", "M"),
  stringsAsFactors = FALSE
)
newPed <- addParents(pedTwo)
newPed
#>   id sire  dam sex recordStatus
#> 1 d1 <NA> <NA>   F     original
#> 2 s2 <NA> <NA>   M     original
#> 3 d2 <NA> <NA>   F     original
#> 4 o1   s1   d1   F     original
#> 5 o2   s1   d2   F     original
#> 6 o3   s2   d2   F     original
#> 7 o4   s2   d2   M     original
#> 8 s1 <NA> <NA>   M        added