Compute the kinship matrix for a set of related autosomal subjects.
The function is generic, and can accept a pedigree, pedigreeList,
or vector as the first argument.
Usage
kinship(id, ...)
## S3 method for class 'pedigree'
kinship(id, chrtype="autosome", ...)
## S3 method for class 'pedigreeList'
kinship(id, chrtype="autosome", ...)
## Default S3 method:
kinship(id, dadid, momid, sex, chrtype="autosome", ...)
Arguments
id
either a pedigree object, pedigreeList object, or a vector of
subject identifiers. Subject identifiers may be numeric or
character.
dadid
for each subject, the identifier of the biological father.
This is only used if id is a vector.
momid
for each subject, the identifier of the biological mother.
This is only used if id is a vector.
sex
vector of sex values coded as 1=male, 2=female
chrtype
chromosome type. The currently supported types
are "autosome" and "X" or "x".
...
Any number of optional arguments
Details
The function will usually be called with a pedigree or pedigreeList;
the third form is provided for backwards compatability with an earlier
release of the library that was less capable.
The first argument is named id
for the same reason. Note that when using the third form any
information on twins is not available to the function.
When called with a pedigreeList, i.e., with multiple families, the
routine will create a block-diagonal-symmetric sparse matrix object
of class dsCMatrix.
Since the [i,j] value of the result is 0 for any two
unrelated individuals i and j and a Matrix utilizes sparse
representation, the resulting object is often orders of magnitude
smaller than an ordinary matrix.
When kinship is called with a single pedigree
an ordinary matrix is returned.
Two genes G1 and G2 are identical by descent (IBD) if they are both physical
copies of the same ancestral gene; two genes are identical by state if
they represent the same allele.
So the brown eye gene that I inherited from my mother is IBD with hers;
the same gene in an unrelated individual is not.
The kinship coefficient between two subjects is the probability that a
randomly selected allele from a locus will be IBD between them.
It is obviously 0 between unrelated individuals.
For an autosomal site and no inbreeding
it will be 0.5 for an individual
with themselves, .25 between mother and child, .125 between an uncle and
neice, etc.
The computation is based on a recursive algorithm described in Lange,
which assumes that the founder alleles are all independent.
Value
a matrix of kinship coefficients.
References
K Lange, Mathematical and Statistical Methods for Genetic Analysis,
Springer-Verlag, New York, 1997.