globalFST: Genome-wide global FST (Weir & Cockerham 1984).

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

Description

This function estimates genom-wide global FST based on Weir and Cockerham's theta (Weir & Cockerham 1984) from a GENEPOP data object (Rousset 2008). Missing genotype values in the GENEPOP file ("0000" or "000000") are simply ignored.

Usage

globalFST(popdata)

Arguments

popdata

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

Value

fst	Estimated genome-wide global FST
se	Standard error 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, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358-1370.

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)

# theta estimation
result.globalFST <- globalFST(popdata)
print(result.globalFST)

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