pegas (version 0.10)

Fst: F-Statistics

Description

This function computes the \(F_{IT}\), \(F_{ST}\) and \(F_{IS}\) for each locus in the data.

Usage

Fst(x, pop = NULL)

Arguments

x

an object of class "loci".

pop

a vector or factor giving the population assignment of each row of x, or a single numeric value specifying which column of x to use as population indicator. By default, the column labelled "population" is used.

Value

A matrix with genes (loci) as rows and the three F-statistics as columns.

Details

The formulae in Weir and Cockerham (1984) are used for each allele, and then averaged within each locus over the different alleles as suggested by these authors.

References

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

Weir, B. S. and Hill, W. G. (2002) Estimating F-statistics. Annual Review of Genetics, 36, 721--750.

See Also

fstat in package hierfstat; package dirmult on CRAN that implements various estimators of the Dirichlet-multinomial distribution, including maximum likekihood and the moments estimator of Weir and Hill (2002); Fst in Biodem that caculates \(F_{ST}\) from a ``kinship matrix''.

Examples

# NOT RUN {
data(jaguar)
Fst(jaguar)
# }