Fst computes the \(F_{IT}\), \(F_{ST}\) and
\(F_{IS}\) for each locus in the data. Rst computes the
\(R_{ST}\) for microsatellites.
Usage
Fst(x, pop = NULL, quiet = TRUE, na.alleles = "")
Rst(x, pop = NULL, quiet = TRUE, na.alleles = "")
Value
A matrix with genes (loci) as rows and the three F-statistics
as columns.
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.
Author
Emmanuel Paradis
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).
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 \(F_{ST}\) from a ``kinship
matrix''.
data(jaguar)
Fst(jaguar)
Rst(jaguar)
## no Fst but Fit and Fis in case of single population:jaguar_corridor <- jaguar[jaguar$population == "Green Corridor", ]
Fst(jaguar_corridor)