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Make a CEPH-style pedigree for each id

Source: R/makeCEPH.R
makeCEPH.Rd

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.

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.}

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
#>