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]