FinePop: GstNC – R documentation

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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.

Author(s)

Reiichiro Nakamichi, Hirohisa Kishino, Shuichi Kitada

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.

Examples

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

FinePop

Fine-Scale Population Analysis

v1.5.1

GPL (>= 2.0)

Authors