R: F-Statistics

Fst {pegas} | R Documentation

## F-Statistics

### Description

`Fst` computes the Fit, Fst and Fis for each locus in the data. `Rst` computes the Rst for microsatellites.

### Usage

    Fst(x, pop = NULL, quiet = TRUE, na.alleles = "")
    Rst(x, pop = NULL, quiet = TRUE, na.alleles = "")

### 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.
`quiet` | a logical value: should calculations be quiet?
`na.alleles` | by default, only genotypes coded as NA are considered as missing data. This option is to specify if some alleles code for missing data.

### Details

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

`Rst` uses the formulae in Slatkin (1995).

### Value

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

### Author(s)

Emmanuel Paradis

### References

Slatkin, M. (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics, 139, 457–462.

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 Fst from a “kinship matrix”.

### Examples

    data(jaguar)
    Fst(jaguar)
    Rst(jaguar)

[Package pegas version 0.13 Index]