pedtools (version 2.8.0)

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)
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)

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 + uncles) and 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).

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. 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

Author

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