SetModels {FEST}R Documentation

Specify true and alternative family relations

Description

Specify true and alternative family relations.

Usage

SetModels(trueModels, altModels = c("true", "unrelated"))

Arguments

trueModels a character array of the true family relations. See details.
altModels a character array of alternative hypothised family relations. See details.

Details

The true and alternative pairwise family relations are among the following:

HS-k-l:
Generalised half-sib relationships where k=1, 2, ... and l=1, 2,... 'HS-k-l' specifies a relation where two persons sharing one common ancestor; one person is k generation apart and the other is l generation apart. Examples: 'HS-1-1' is a half-sib relation, 'HS-2-2' specifies two persons sharing a grandparent.
HS-k:
Same as HS-k-k
S-k-l:
Generalised sibling relationships where k=1, 2 ... and l=1, 2,... 'S-k-l' specifies a relation where two persons are sharing one common ancestor; one person is k+1 generation apart and the other is l+1 generation apart. Examples: 'S-1-1' specifies sibs, 'S-2-2' first cousins, 'S-1-2' an uncle-niece relation.
S-k:
Same as S-k-k
PC-k:
Generalised sibling relationships where k=1, 2 ... 'PC-k' specifies a relation where the second person is the ancestor of first person, k generations apart. Examples: 'PC-1' specifies a parent-child relation, 'PC-2' a grandparent-grandchild relation.
unrelated:
Two unrelated persons

In addition altModels may also contain the following specifications:

true:
Same models as specified in trueModels
upper:
A generation-less relation than the true model specified in trueModels
lower:
A generation-more relation than the true model specified in trueModels

The available family relations are constrained by default setting in merling for maximal allowed pedigree complexity allowed by merlin http://www.sph.umich.edu/csg/abecasis/Merlin/index.html. For the moment we allow HS-k-l and S-k-l where k+l<= 25, and PC-k where k <= 25.

Value

An object of class Model.

Author(s)

Øivind Skare oivind.skare@medisin.uio.no

See Also

Model

Examples

## Example 1
  modelList <- paste("HS-", 1:5, sep="")
  models <- SetModels(trueModels=modelList, altModels=c(modelList, "unrelated"))
## Example 2
  models <- SetModels(trueModels=paste("HS-", 1:6, sep=""),
                      altModels=c("true", "unrelated"))

[Package FEST version 0.06 Index]