FinePop (version 1.1.1)

EBFST: Empirical Bayes estimator of Fst.

Description

This function estimates global/pairwise Fst among subpopulations using empirical Bayes method (Kitada et al. 2007). Preciseness of estimated pairwise Fst is evaluated by bootstrap method.

Usage

EBFST(popdata)

Arguments

popdata

Population data object created by read.genepop function from a GENEPOP file (Rousset 2008).

Value

global:pairwise:

References

Kitada S, Kitakado T, Kishino H (2007) Empirical Bayes inference of pairwise FST and its distribution in the genome. Genetics, 177, 861-873. Rousset F (2008) Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Resources, 8, 103-106.

See Also

read.genepop, as.dist, as.dendrogram, hclust, cmdscale, nj

Examples

# data
data(data.JSM)
cat(data.JSM$genepop, file="JSM_genepop.txt", sep="\n")
cat(data.JSM$popname, file="JSM_popname.txt", sep=" ")
popdata <- read.genepop(genepop="JSM_genepop.txt", popname="JSM_popname.txt")

# Fst estimation
result.eb <- EBFST(popdata)
ebfst <- result.eb$pairwise$fst
write.csv(ebfst, "result_EBFST.csv", na="")

# dendrogram
ebfst.d <- as.dist(ebfst)
ebfst.hc <- hclust(ebfst.d,method="average")
plot(as.dendrogram(ebfst.hc), xlab="",ylab="",main="", las=1)

# MDS plot
mds <- cmdscale(ebfst.d)
plot(mds, type="n", xlab="",ylab="")
text(mds[,1],mds[,2], popdata$pop_names)

# NJ tree
library(ape)
ebfst.nj <- nj(ebfst.d)
plot(ebfst.nj,type="u",main="",sub="")