Fst: F-Statistics

In dwinter/Pegas: Population and Evolutionary Genetics Analysis System

Description

This function computes the Fit, Fst and Fis 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.

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.

Value

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

Note

Programming bugs have been fixed in version 0.3-2 of pegas. Further tests and feed-back are still welcome.

Author(s)

Emmanuel Paradis

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. Annu Review of Genetics, 36, 721–750.

See Also

fstat in adegenet; 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 Fst from a “kinship matrix”.

Examples

require(adegenet)
data(nancycats)
x <- as.loci(nancycats)
Fst(x)

dwinter/Pegas documentation built on May 15, 2019, 6:21 p.m.