adegenet (version 1.2-7)

F statistics: F statistics for genind objects

Description

The function fstat computes a global Fst, while pairwise.fst computes Nei's pairwise Fst between all pairs of populations. Both functions are designed for genind objects.

fstat is wrapper for varcomp.glob from package hierfstat for genind objects. It computes F statistics (Fst, Fis, Fit) given a set of genotypes and a grouping factor.

pairwise.fst is an implementation of Nei's Fst in which heretozygosities are weighted by group sizes (see details).

Usage

fstat(x, pop=NULL, fstonly=FALSE)
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'.

fstonly

a logical stating whether only the Fst value should be returned (TRUE) instead of all F statistics (FALSE, default).

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, varcomp.glob, gstat.randtest

Examples

if(require(hierfstat)){
data(nancycats)

## Fst, Fis, Fit
fstat(nancycats)

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