F-Statistics
Fst computes the Fit, Fst and
Fis for each locus in the data. Rst computes the
Rst for microsatellites.
Fst(x, pop = NULL, quiet = TRUE, na.alleles = "") Rst(x, pop = NULL, quiet = TRUE, na.alleles = "")
x |
an object of class |
pop |
a vector or factor giving the population assignment of each
row of |
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. |
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).
A matrix with genes (loci) as rows and the three F-statistics as columns.
Emmanuel Paradis
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.
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”.
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)
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