calculate.pairwise.Fst {BEDASSLE} | R Documentation |
This function calculates unbiased F_{ST}
(based on Weir and Hill's
\theta
, 2002), between a pair of populations/individuals. Loci for which either
of the populations/individuals has missing data (i.e. - the sample size is zero) are
excluded.
calculate.pairwise.Fst(allele.counts, sample.sizes)
allele.counts |
A matrix of allele counts of dimensions |
sample.sizes |
A matrix of sample sizes of dimensions |
Pairwise unbiased F_{ST}
between a pair of populations/individuals
Gideon Bradburd
Weir,B.S. and W.G. Hill. 2002. Estimating F-statistics. Ann.Rev.Gen. 36:949-952.
#With the HGDP dataset
data(HGDP.bedassle.data)
#Draw 2 populations at random from the Eurasian HGDP dataset
pop1 <- sample(nrow(HGDP.bedassle.data$allele.counts),1)
pop2 <- sample(nrow(HGDP.bedassle.data$allele.counts),1)
#Calculate unbiased Fst between them
pairwise.Fst <- calculate.pairwise.Fst(
HGDP.bedassle.data$allele.counts[c(pop1,pop2),],
HGDP.bedassle.data$sample.sizes[c(pop1,pop2),]
)
#Print that Fst to the console
print(sprintf("Fst between the %s population and the %s population is %s",
HGDP.bedassle.data$hgdp.metadata[pop1,1],
HGDP.bedassle.data$hgdp.metadata[pop2,1],
round(pairwise.Fst,3))
)