gen.f: 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))

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.

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.

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.

Examples

Run this code

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))

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