ped_subgroups {pedtools}R Documentation

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)

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)

niblings(x, id, half = NA, internal = FALSE)

piblings(x, id, half = NA, internal = FALSE)

ancestors(x, id, maxGen = Inf, inclusive = FALSE, internal = FALSE)

commonAncestors(x, ids, maxGen = Inf, inclusive = FALSE, internal = FALSE)

descendants(x, id, maxGen = Inf, inclusive = FALSE, internal = FALSE)

commonDescendants(x, ids, maxGen = Inf, inclusive = FALSE, internal = FALSE)

descentPaths(x, ids = founders(x), internal = FALSE)

Arguments

x

A ped() object or a list of such.

internal

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

id, ids

A character (or coercible to character) of one or more ID labels. If internal is TRUE, id and ids should be positive integers.

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.

maxGen

The number of generations to include. Default: Inf (no limit).

inclusive

A logical indicating whether an individual should be counted among his or her own ancestors/descendants

Value

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, parents, children, siblings, grandparents, spouses, niblings (nephews + nieces), piblings (aunts

The commands ancestors(x, id) and descendants(x, id) return vectors 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, otherwise not. To cut off at a specific number of generations, use maxGen.

For commonAncestors(x, ids) and commonDescendants(x, ids), the output is a vector containing the IDs of common ancestors (descendants) to all of ids.

Finally, descentPaths(x, ids) returns a list of lists, containing all pedigree paths descending from each individual in ids (by default all founders).

Author(s)

Magnus Dehli Vigeland

Examples


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
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

niblings(x, 9) # 6, 7
niblings(x, 9, half = FALSE) # none

piblings(x, 6) # 9
piblings(x, 6, half = FALSE) # none

ancestors(x, 6)                               # 2, 3, 4, 5
ancestors(x, 6, maxGen = 2, inclusive = TRUE) # 4, 5, 6

descendants(x, 2)                                # 4, 6, 7, 9
descendants(x, 2, maxGen = 2, inclusive = TRUE)  # 2, 4, 9

leaves(x)          # 6, 7, 9
founders(x)        # 2, 3, 5, 8


[Package pedtools version 2.8.2 Index]