ped_subgroups: Pedigree subgroups

In magnusdv/pedtools: Creating and Working with Pedigrees and Marker Data

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)

nephews_nieces(x, id, removal = 1, 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 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.
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, 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.

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

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

magnusdv/pedtools documentation built on April 9, 2024, 7:35 a.m.