Computes F statistics on the output of an inference by MCMC simulation

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Description

Computes F statistics according to Weir and Cockerham's estimators. Missing values are allowed but as of today, the NA code is only treated as an extra allele which might bias the result. This function should not be used on haploid data.

Usage

1
Fstat.output(coordinates,genotypes,ploidy,burnin,path.mcmc)

Arguments

coordinates

Matrix with one line per individual and two columns

genotypes

Genotypes of individuals. A matrix with one line per individual and 2 columns per locus

burnin

Integer: number of saved iterations to discard.

ploidy

Integer: 1 or 2 (default is 2). Do not use for haploid data.

path.mcmc

Path to output files directory

Value

A list with components

Pairwise.Fis

A matrix of real numbers estimating the pairwise Fis

Pairwise.Fst

A matrix of real numbers estimating the pairwise Fst

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.

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