Fst {Geneclust}R Documentation

F statistics

Description

Computes F statistics according to Weir and Cockerham's estimators.

Usage

Fst(genotypes, allele.numbers, pop.mbrship, npopmax)

Arguments

genotypes Genotypes of individuals. A matrix with one line per individual and 2 columns per locus
allele.numbers A vector of integer that containis the number of alleles at each locus
pop.mbrship A vector of integer that contains the posterior cluster labels (assignments)
npopmax A likely maximal number of clusters in the population

Value

A list with components

Total.Fit A real number estimating the total Fit
Pairwise.Fis A matrix of real numbers estimating the pairwise Fis
Pairwise.Fst A matrix of real numbers estimating the pairwise Fst
Pairwise.Fit A matrix of real numbers estimating the pairwise Fit

Author(s)

Arnaud Estoup for original code in Turbo Pascal. Translation in Fortran and interface with R by Gilles Guillot

References

Weir, B.S. and C.C. Cockerham, Estimating F-statistics for the analysis of population structure, Evolution, 1984, vol. 38, 1358-1370.

Examples

## see also the example described in the function mcmcgeneclust

## Not run: 
data(bear)

hc <- hgclust(bear, K=4)
plot(hc)

n.all <- c(3,3,5,6,6,6,6,7,7,7,7,7,8,8,8,8,10,10,10)

Fst(as.matrix(bear)[,3:40], n.all, hc$labels, npopmax=4)$Pairwise.Fst

## End(Not run)


[Package Geneclust version 1.0.0 Index]