Make a CEPH-style pedigree for each id

Part of Relations

Usage

makeCEPH(id, sire, dam)

Arguments

id

character vector of the unique identifiers of all individuals; a duplicated id stops the function with a duplicate row.names error.

sire

character vector, parallel to id, with the identifier of each individual's father (NA if unknown).

dam

character vector, parallel to id, with the identifier of each individual's mother (NA if unknown).

Value

List of lists: fields: id, subfields: parents, pgp, mgp. Pedigree information converted into a CEPH-style list. The top level list elements are the IDs from id. Below each ID is a list of three elements: parents (sire, dam), paternal grandparents (pgp: sire, dam), and maternal grandparents (mgp: sire, dam).

Details

Creates a CEPH-style pedigree for each id, consisting of three generations: the id, the parents, and the grandparents. Inserts NA for unknown pedigree members.

Examples

library(nprcgenekeepr)
ped <- nprcgenekeepr::lacy1989Ped
pedCEPH <- makeCEPH(ped$id, ped$sire, ped$dam)
head(ped)
#>   id sire  dam gen population
#> 1  A <NA> <NA>   0       TRUE
#> 2  B <NA> <NA>   0       TRUE
#> 3  C    A    B   1       TRUE
#> 4  D    A    B   1       TRUE
#> 5  E <NA> <NA>   0       TRUE
#> 6  F    D    E   2       TRUE
head(pedCEPH$F)
#> $parents
#> [1] "D" "E"
#> 
#> $pgp
#> [1] "A" "B"
#> 
#> $mgp
#> [1] NA NA
#>