Inbreeding coefficient

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Description

Returns the inbreeding coefficients of the specified probands

Usage

1
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

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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")

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