fst: Compute the F_{ST} for a Sample of Genes

In infeR: A pedagogical tool to teach the basics of inference in population genetics

Description

Compute the F_ST for a sample of genes.

Usage

  fst(sample)

Arguments

sample

an object generated by the sim.inference.model or by the sim.coalescent commands

Details

Once the sim.inference.model or by the sim.coalescent command lines have been executed, fst can be used to compute the Weir and Cockerham's (1984) estimate of F_ST for that sample. The multilocus estimator of F_ST is computed as in Genepop (Rousset 2008).

Value

Weir and Cockerham's (1984) estimate of F_ST for the sample of genes contained in the object ‘sample’

References

Rousset, F. (2008) genepop'007: a complete re-implementation of the genepop software for Windows and Linux, Molecular Ecology Notes 8: 103-106.

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

Examples

## This is to simulate a sample of genes (at a single locus), using the inference model, with
## 50 genes collected in each of 10 sampled demes. In this example, the product of
## twice the effective population size and migration rate is 2, 
## and the frequency of allele A in the migrant pool is 0.5

sample <- sim.inference.model(number.of.sampled.demes = 10,sample.sizes = 50,M = 2,pi = 0.5)

## This is to compute Weir and Cockerham's (1984) estimate for that sample

fst(sample)

infeR documentation built on May 2, 2019, 4:45 p.m.