calculate.all.pairwise.Fst {BEDASSLE} | R Documentation |
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.
calculate.all.pairwise.Fst(allele.counts, sample.sizes)
allele.counts |
A matrix of allelic count data, for which |
sample.sizes |
A matrix of sample sizes, for which |
A matrix of pairwise, unbiased F_{ST}
.
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)
#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"))