pop_pairwiseFST: Genome-wide poppulation-paiwise FST (Nei & Chesser 1983).

In FinePop2: Fine-Scale Population Analysis (Rewrite for Gene-Trait-Environment Interaction Analysis)

Description

This function estimates genome-wide poppulation-paiwise FST among subpopulations based on Nei and Chesser's corrected GST (Nei&Chesser 1983) from a GENEPOP data object (Rousset 2008). Missing genotype values in the GENEPOP file ("0000" or "000000") are simply ignored.

Usage

pop_pairwiseFST(popdata)

Arguments

popdata

Population data object created by read.GENEPOP function from a GENEPOP file.

Value

Estimated genome-wide population-pairwise FST.

Author(s)

Reiichiro Nakamichi, Shuichi Kitada, Hirohisa Kishino

References

Nei M, Chesser RK (1983) Estimation of fixation indices and gene diversity. Annals of Human Genetics, 47, 253-259.

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

Examples

# Example of GENEPOP file
data(jsmackerel)
jsm.ms.genepop.file <- tempfile()
jsm.popname.file <- tempfile()
cat(jsmackerel$MS.genepop, file=jsm.ms.genepop.file, sep="\n")
cat(jsmackerel$popname, file=jsm.popname.file, sep=" ")

# Data load
# Prepare your GENEPOP file and population name file in the working directory.
# Replace "jsm.ms.genepop.file" and "jsm.popname.file" by your file names.
popdata <- read.GENEPOP(genepop=jsm.ms.genepop.file, popname=jsm.popname.file)

# GST estimation
result.poppairFST <- pop_pairwiseFST(popdata)
poppairFST.d <- as.dist(result.poppairFST)
print(poppairFST.d)

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

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

FinePop2 documentation built on March 26, 2020, 9:01 p.m.