pop_specificFST: Genome-wide population-specific FST (Weir & Goudet 2017).

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

Description

This function estimates genome-wide poppulation-specific FST based on Weir and Goudet's Method (Weir&Goudet 2017) from a GENEPOP data object (Rousset 2008). Missing genotype values in the GENEPOP file ("0000" or "000000") are simply ignored.

Usage

pop_specificFST(popdata, cov = FALSE)

Arguments

popdata	Population data object created by read.GENEPOP function from a GENEPOP file.
cov	A Logical argument indicating whether variance-covariance matrix of estimated FST should be calculated.

Value

fst	Estimated genome-wide population-specific FST and standard error.
cov	Variance-covariance matrix of estimated FST

Author(s)

Reiichiro Nakamichi, Shuichi Kitada, Hirohisa Kishino

References

Rousset F (2008) Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Resources, 8, 103-106.

Weir BS, Goudet J (2017) A Unified Characterization of Population Structure and Relatedness. Genetics, 206, 2085-2103.

See Also

read.GENEPOP

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
result.popspFST <- pop_specificFST(popdata)
print(result.popspFST$fst)

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