FinePop (version 1.3.0)

GstNC: Nei and Chesser's Gst

Description

This function estimates pairwise Gst among subpopulations (Nei&Chesser 1983) from a GENEPOP data object (Rousset 2008). Missing genotype values in the GENEPOP file ("0000" or "000000") are simply ignored.

Usage

GstNC(popdata)

Arguments

popdata

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

Value

Matrix of estimated pairwise Gst.

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

Examples

# Example of GENEPOP file
data(data.JSM)
cat(data.JSM$MS.genepop, file="JSM_MS_genepop.txt", sep="\n")
cat(data.JSM$popname, file="JSM_popname.txt", sep=" ")

# Data load
# Prepare your GENEPOP file and population name file in the working directory
# (Here, these files were provided as "JSM_MS_genepop.txt" and "JSM_popname.txt".)
popdata <- read.genepop(genepop="JSM_MS_genepop.txt", popname="JSM_popname.txt")

# Gst estimation
result.gstNC <- GstNC(popdata)
write.csv(result.gstNC, "result_GstNC.csv", na="")
print(as.dist(result.gstNC))