R: Kinship coefficient

gen.phi {GENLIB} | R Documentation

## Kinship coefficient

### Description

Returns the kinship coefficients between pairs of individuals

### Usage

    gen.phi(gen, pro, depthmin=(gen.depth(gen)-1), depthmax=(gen.depth(gen)-1), MT=F)

### Arguments

`gen` | An object of class GLgen obtained with gen.genealogy, gen.lineages or gen.branching. Required.
`pro` | Vector of proband id numbers to be included. Required.
`depthmin` | Minimum genealogical depth to consider in the calculation. Default is the whole genealogy.
`depthmax` | Maximum genealogical depth to consider in the calculation. Default is the whole genealogy.
`MT` | Allows parallel computing when set to TRUE. Default is MT=F.

### Value

A matrix or a GLmultiMatrix object depending on the number of generations treated. GLmultiMatrix is an array of matrices, one for each depth. Array of size ('depthMax'-'depthMin') and matrices of size 'length(pro)' * 'length(pro)'. The matrix object, also of size 'length(pro)' * 'length(pro)', is returned when ('depthMax'-'depthMin') equals 1.

### References

Malecot G. (1948) Les mathematiques de l'heredite. Paris: Masson, p 65.

Thompson EA. (1986) Pedigree Analysis in Human Genetics. Baltimore, MD, USA: Johns Hopkins University Press, p 25.

Karigl G. (1981) A recursive algorithm for the calculation of identity coefficients. Ann Hum Genet 45:299-305.

### See Also

`gen.genealogy` `gen.f`

### Examples

    data(geneaJi)
    genJi<-gen.genealogy(geneaJi)
    kinship<-gen.phi(genJi)
    kinship

    kinship_allgenerations<-gen.phi(genJi, depthmin =1)
    kinship_allgenerations
    ## Not run: 7th generations back in time is equivalent to considering all generations
    kinship_allgenerations <- unclass(kinship_allgenerations)
    kinship_allgenerations[,,7]==kinship

    kinship_allgenerations[1,2,]

    ## Not run: Plot of kinship varying according to number of generations considered
    plot(1:7,kinship_allgenerations[1,2,], type="b", xlab="Generation", ylab="Kinship value",
         ylim=c(0,0.6), pch=0)
    points(1:7,kinship_allgenerations[1,3,], type="b", lty=12, pch=1)
    legend("topright", legend=c("Individuals 1 and 2", "Individuals 2 and 29"),lty=c(1,12), pch=c(0,1))

[Package GENLIB version 1.0.6 Index]