calculate.pairwise.Fst {BEDASSLE} R Documentation

Calculates unbiased pairwise Fst between a pair of populations

Description

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.

Usage

calculate.pairwise.Fst(allele.counts, sample.sizes)


Arguments

 allele.counts A matrix of allele counts of dimensions nrow =  2, one for each of the two populations/individuals between which pairwise F_{ST} is being calculated, and ncol =  the number of loci genotyped. sample.sizes A matrix of sample sizes of dimensions nrow =  2, one for each of the two populations/individuals between which pairwise F_{ST} is being calculated, and ncol =  the number of loci genotyped (i.e. - the dimensions of sample.sizes must match those of counts). Each cell gives the number of chromosomes successfully genotyped at each locus in each population.

Value

Pairwise unbiased F_{ST} between a pair of populations/individuals

References

Weir,B.S. and W.G. Hill. 2002. Estimating F-statistics. Ann.Rev.Gen. 36:949-952.

Examples

#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))
)


[Package BEDASSLE version 1.6.1 Index]