makeCEPH {nprcgenekeepr}R Documentation

Make a CEPH-style pedigree for each id

Description

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).

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.

Calculates the first-order relationships in a pedigree, and to convert pairwise kinships to the appropriate relationship category. Relationships categories: For each ID in the pair, find a CEPH-style pedigree and compare them

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).

Examples

library(nprcgenekeepr)
ped <- nprcgenekeepr::lacy1989Ped
pedCEPH <- makeCEPH(ped$id, ped$sire, ped$dam)
head(ped)
head(pedCEPH$F)

[Package nprcgenekeepr version 1.0.7 Index]