gen.phi {GENLIB}

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=FALSE)

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=FALSE.

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
# 7th generations back in time is equivalent to considering all generations
kinship_allgenerations <- unclass(kinship_allgenerations)
kinship_allgenerations[,,7]==kinship

kinship_allgenerations[1,2,]

# 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))