R: Inbreeding coefficient

gen.f {GENLIB} | R Documentation

## Inbreeding coefficient

### Description

Returns the inbreeding coefficients of the specified probands

### Usage

    gen.f( gen, pro, depthmin= (gen.depth(gen)-1), depthmax= (gen.depth(gen)-1))

### 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.
`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.

### Value

A vector or GLmultiVector object depending on the number of generations treated. GLmultiVector is an array of vectors, one for each depth. Array of size ('depthMax'-'depthMin'), vectors of size 'length(pro)'. A vector of size '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.phi`

### Examples

    data(geneaJi)
    genJi<-gen.genealogy(geneaJi)
    f_values<-gen.f(genJi)
    f_values
    f_allgen<-gen.f(genJi, depthmin=1)
    f_allgen<-unclass(f_allgen)

    plot(1:7,f_allgen[1,],type="b",xlab="Generation",ylab="Inbreeding values",ylim=c(0,0.25),pch=0)
    points(1:7,f_allgen[3,],  type="b", lty=12, pch=1)
    legend("topright", legend=c("Individual 1", "Individual 29"),lty=c(1,12), pch=c(0,1))

    data(genea140)
    gen140<-gen.genealogy(genea140)
    inbreeding_val<-gen.f(gen140)
    boxplot(inbreeding_val, horizontal=TRUE, xlab="Inbreeding values")

[Package GENLIB version 1.0.6 Index]