calcFst: Calculate Fst statistics for frequency data

calcFstR Documentation

Calculate Fst statistics for frequency data

Description

Calculates Weir and Cockerham's Fst for frequency data

Usage

calcFst(data, grps)

Arguments

You can put normal text in Arguments, too, like this. Remember to indent all arguments, as below.

data

a nMarker by nAnimal matrix of allele frequencies. That is for animal i and codominant marker j data[j,i] is the number of copies of the SNP allele (0, 1, or 2).

grps

a numeric vector giving the populations of the nAnimals

Details

This function is really just a wrapper for the Fstat() function, taken from the (now unsupported) Geneland package.

Value

A numeric matrix containing the pairwise Fst values between all populations.

Authors

Arnaud Estoup for original code in Turbo Pascal. Translation in Fortran and interface with R by Gilles Guillot (for Geneland package). Scott Foster for latest wrapper for stockR package.

Author(s)

Scott D. Foster

Examples

set.seed(717)
data <- sim.stock.data( nAnimals=50, nSNPs=500, nSampleGrps=50, K=5, ninform=50)
calcFst( data, attributes( data)$grps)

stockR documentation built on April 26, 2023, 9:13 a.m.

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