kinship: Compute a kinship matrix

In kinship2: Pedigree Functions

Compute a kinship matrix

Description

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.

See Also

pedigree, makekinship,makefamid

Examples

test1 <- data.frame(id  =c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14),
                    mom =c(0, 0, 0, 0, 2, 2, 4, 4, 6,  2,  0,  0, 12, 13),
                    dad =c(0, 0, 0, 0, 1, 1, 3, 3, 3,  7,  0,  0, 11, 10),
                    sex =c(0, 1, 0, 1, 0, 1, 0, 1, 0,  0,  0,  1,  1,  1))
tped <- with(test1, pedigree(id, dad, mom, sex))
round(8*kinship(tped))

kinship2 documentation built on May 29, 2024, 11:14 a.m.