calculate.all.pairwise.Fst {BEDASSLE} R Documentation

## Calculates unbiased pairwise Fst between all sampled populations

### Description

This function calculates unbiased F_{ST} (based on Weir and Hill's \theta, 2002), between all populations/individuals included in the counts matrix, and returns the results in a k by k matrix, where k = nrow(counts). Loci for which either of the populations/individuals has missing data (i.e. - the sample size is zero) are excluded.

### Usage

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


### Arguments

 allele.counts A matrix of allelic count data, for which nrow =  the number of populations and ncol =  the number of bi-allelic loci sampled. Each cell gives the number of times allele ‘1’ is observed in each population. The choice of which allele is allele ‘1’ is arbitrary, but must be consistent across all populations at a locus. sample.sizes A matrix of sample sizes, for which nrow =  the number of populations and ncol =  the number of bi-allelic loci sampled (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

A matrix of pairwise, unbiased F_{ST}.

### 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)

#Calculate pairwise Fst between all population pairs
hgdp.pairwise.Fst <- calculate.all.pairwise.Fst(
HGDP.bedassle.data$allele.counts, HGDP.bedassle.data$sample.sizes
)

#Plot pairwise Fst against geographic distance
plot(HGDP.bedassle.data$GeoDistance, hgdp.pairwise.Fst, pch=19, col=HGDP.bedassle.data$EcoDistance+1,
ylab="pairwise Fst",
xlab="geographic distance",
main="isolation by distance")
legend(x="bottomright",pch=19,col=c(1,2),
legend=c("same side of Himalayas",
"opposite sides of Himalayas"))


[Package BEDASSLE version 1.6 Index]