FinePop: GstH – R documentation

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GstH

Hedrick's G'st

Description

This function estimates pairwise G'st (Hedrick 2005) among subpopulations from a GENEPOP data object (Rousset 2008). Missing genotype values in the GENEPOP file ("0000" or "000000") are simply ignored.

Usage

GstH(popdata)

Arguments

popdata

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

Value

Matrix of estimated pairwise Hedrick's G'st.

Author(s)

Reiichiro Nakamichi, Hirohisa Kishino, Shuichi Kitada

References

Hedrick P (2005) A standardized genetic differentiation measure. Evolution, 59, 1633-1638.

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")

# Hedrick's G'st estimation
result.GstH <- GstH(popdata)
write.csv(result.GstH, "result_GstH.csv", na="")
print(as.dist(result.GstH))

FinePop

Fine-Scale Population Analysis

v1.5.1

GPL (>= 2.0)

Authors