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 ( |
dam |
character vector with unique identifier for an
individual's mother ( |
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
{If one is the parent of the other} {— Designate the relationship as
parent-offspring
}{Else if both parents are shared} {— Designate the relationship as
full-siblings
}{Else if one parent is shared} {— Designate the relationship as
half-siblings
}{Else if one is the grandparent of the other} {— Designate the relationship as
grandparent-grandchild
}{Else if both grand parents are shared} {— Designate the relationship as
cousin
}{Else if at least one grand parent is shared} {— Designate the relationship as
cousin - other
}{Else if the parents of one are the grandparents of the other} {— Designate the relationship as
full-avuncular
}{Else if a single parent of one is the grandparent of the other} {— Designate the relationship as
avuncular - other
}{Else if the kinship is greater than 0, but the pair don't fall into the above categories} {— Designate the relationship as
other
}{Else} {— Designate the relationships as
no relation.
}
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)