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

dataframe that is the Pedigree. The id, sire, dam and sex columns are required.

Value

An updated pedigree with entries added as necessary. Entries have the id and sex specified; all remaining columns except recordStatus are filled with NA. A recordStatus column is added (replacing any existing one) with "original" for the existing records and "added" for the new ones.

Details

This must be run after 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