locus_specificFST: Locus-specific global FST (Kitada et al. 2007, 2017).

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

Description

This function estimates locus-specific global FST among subpopulations using empirical Bayes method (Kitada et al. 2007, 2017) from a GENEPOP data object (Rousset 2008). Missing genotype values in the GENEPOP file ("0000" or "000000") are simply ignored.

Usage

locus_specificFST(popdata)

Arguments

popdata

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

Value

Estimated locus-specific global FST.

Author(s)

Reiichiro Nakamichi, Shuichi Kitada, Hirohisa Kishino

References

Kitada S, Kitakado T, Kishino H (2007) Empirical Bayes inference of pairwise FST and its distribution in the genome. Genetics, 177, 861-873.

Kitada S, Nakamichi R, Kishino H (2017) The empirical Bayes estimators of fine-scale population structure in high gene flow species. Mol. Ecol. Resources, DOI: 10.1111/1755-0998.12663

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, read.frequency

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)

# FST estimation
locspFST <- locus_specificFST(popdata)
print(locspFST)

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