Pedigree subgroups
A collection of utility functions for identifying pedigree members with certain properties.
founders(x, internal = FALSE) nonfounders(x, internal = FALSE) leaves(x, internal = FALSE) males(x, internal = FALSE) females(x, internal = FALSE) typedMembers(x, internal = FALSE) untypedMembers(x, internal = FALSE) father(x, id, internal = FALSE) mother(x, id, internal = FALSE) children(x, id, internal = FALSE) offspring(x, id, internal = FALSE) spouses(x, id, internal = FALSE) unrelated(x, id, internal = FALSE) parents(x, id, internal = FALSE) grandparents(x, id, degree = 2, internal = FALSE) siblings(x, id, half = NA, internal = FALSE) nephews_nieces(x, id, removal = 1, half = NA, internal = FALSE) ancestors(x, id, inclusive = FALSE, internal = FALSE) commonAncestors(x, ids, inclusive = FALSE, internal = FALSE) descendants(x, id, inclusive = FALSE, internal = FALSE) commonDescendants(x, ids, inclusive = FALSE, internal = FALSE)
x |
A |
internal |
A logical indicating whether |
id, ids |
A character (or coercible to such) with one or several ID labels. |
degree, removal |
Non-negative integers. |
half |
a logical or NA. If TRUE (resp FALSE), only half (resp. full) siblings/cousins/nephews/nieces are returned. If NA, both categories are included. |
inclusive |
A logical indicating whether an individual should be counted among his or her own ancestors/descendants |
The functions ancestors(x, id) and descendants(x, id) return a
vector containing the IDs of all ancestors (resp. descendants) of the
individual id within the pedigree x. If inclusive = TRUE, id is
included in the output.
For commonAncestors(x, ids) and commonDescendants(x, ids), a vector
containing the IDs of common ancestors to all of ids.
The functions founders, nonfounders, males, females, leaves each
return a vector containing the IDs of all pedigree members with the wanted
property. (Recall that a founder is a member without parents in the
pedigree, and that a leaf is a member without children in the pedigree.)
The functions father, mother, cousins, grandparents,
nephews_nieces, children, parents, siblings, spouses,
unrelated, each returns a vector containing the IDs of all pedigree
members having the specified relationship with id.
Magnus Dehli Vigeland
x = ped(id = 2:9,
fid = c(0,0,2,0,4,4,0,2),
mid = c(0,0,3,0,5,5,0,8),
sex = c(1,2,1,2,1,2,2,2))
spouses(x, id = 2) # 3, 8
children(x, 2) # 4, 9
descendants(x, 2) # 4, 6, 7, 9
siblings(x, 4) # 9 (full or half)
unrelated(x, 4) # 5, 8
father(x, 4) # 2
mother(x, 4) # 3
siblings(x, 4, half = FALSE) # none
siblings(x, 4, half = TRUE) # 9
leaves(x) # 6, 7, 9
founders(x) # 2, 3, 5, 8Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.