thetaWC.pair: Weir and Cockerham's theta adapted for pairwise Fst.

Description Usage Arguments Details Value Author(s) References See Also Examples

Description

This function estimates Fst between population pairs based on Weir and Cockerham's theta (Weir & Cockerham 1984) adapted for pairwise comparison from a GENEPOP data object (Rousset 2008). Missing genotype values in the GENEPOP file ("0000" or "000000") are simply ignored.

Usage

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thetaWC.pair(popdata)

Arguments

popdata

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

Details

Weir and Cockerham (1984) derived an unbiased estimator of a coancestry coefficient (theta) based on a random effect model. It expresses the extent of genetic heterogeneity within the population. The second stage common approach is to investigate the detailed pattern of the population structure, based on a measure of genetic difference between pairs of subpopulations (demes). We call this by pairwise Fst. This function follows the formula of Weir and Cockerham's theta with the sample size r = 2. Given the pair, our finite sample correction multiplies a of Weir & Cockerham's theta by (r - 1) / r (equation 2 in p.1359 of Weir & Cockerham 1984).

Value

Matrix of estimated pairwise Fst by theta with finite sample correction.

Author(s)

Reiichiro Nakamichi, Hirohisa Kishino, Shuichi Kitada

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

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# 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")

# theta estimation
result.theta.pair <- thetaWC.pair(popdata)
write.csv(result.theta.pair, "result_thetaWCpair.csv", na="")
print(as.dist(result.theta.pair))


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