adegenet (version 1.3-2)

F statistics: F statistics for genind objects

Description

pairwise.fst computes Nei's pairwise Fst between all pairs of populations using a genind object. Heretozygosities are weighted by group sizes (see details).

The function fstat is no longer available as the package hierfstat has been removed from CRAN. For Fst, Fis and Fit, use the function Fst from the pagas package (see example).

Usage

pairwise.fst(x, pop=NULL, res.type=c("dist","matrix"), truenames=TRUE)

Arguments

x

an object of class genind.

pop

a factor giving the 'population' of each individual. If NULL, pop is seeked from pop(x). Note that the term population refers in fact to any grouping of individuals'.

res.type

the type of result to be returned: a dist object, or a symmetric matrix

truenames

a logical indicating whether true labels (as opposed to generic labels) should be used to name the output.

Value

• A vector, a matrix, or a dist object containing F statistics.

encoding

UTF-8

Details

Let $A$ and $B$ be two populations of population sizes $n_A$ and $n_B$, with expected heterozygosity (averaged over loci) $Hs(A)$ and $Hs(B)$, respectively. We denote $Ht$ the expected heterozygosity of a population pooling $A$ and $B$. Then, the pairwise $Fst$ between $A$ and $B$ is computed as: $Fst(A,B) = \frac{(Ht - (n_A Hs(A) + n_B Hs(B))/(n_A + n_B) )}{Ht}$

References

Nei, M. (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA, 70: 3321-3323

See Also

Hs

Examples

## pairwise Fst
mat.fst <- pairwise.fst(nancycats, res.type="matrix")
mat.fst

## Fst, Fis, Fit
if(require(pegas)){
data(nancycats)

## conversion to pegas's format
as.loci(nancycats)

## use Fst from pegas
fsttab <- Fst(as.loci(nancycats))

## average over loci
apply(fsttab, 2, mean)
}