Fst {Geneclust} | R Documentation |
Computes F statistics according to Weir and Cockerham's estimators.
Fst(genotypes, allele.numbers, pop.mbrship, npopmax)
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 |
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 |
Arnaud Estoup for original code in Turbo Pascal. Translation in Fortran and interface with R by Gilles Guillot
Weir, B.S. and C.C. Cockerham, Estimating F-statistics for the analysis of population structure, Evolution, 1984, vol. 38, 1358-1370.
## 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)