Make a CEPH-style pedigree for each id

Part of Relations

Usage

makeCEPH(id, sire, dam)

Arguments

id

character vector with unique identifier for an individual

sire

character vector with unique identifier for an individual's father (NA if unknown).

dam

character vector with unique identifier for an 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
#>