pedtools (version 0.9.6)

ped_subgroups: Pedigree subgroups

Description

A collection of utility functions for identifying pedigree members with certain properties.

Usage

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)
cousins(x, id, degree = 1, removal = 0, 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)

Arguments

x

A ped() object.

internal

A logical indicating whether id (or ids) refers to the internal order.

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

Value

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.

Examples

# NOT RUN {
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))
stopifnot(setequal(spouses(x, 2), c(3,8)),
          setequal(children(x, 2), c(4,9)),
          setequal(descendants(x, 2), c(4,6,7,9)),
          setequal(leaves(x), c(6,7,9)))

# }