GstNC | R Documentation |
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.
GstNC(popdata)
popdata |
Population data object created by read.genepop function from a GENEPOP file. |
Matrix of estimated pairwise Gst.
Reiichiro Nakamichi, Hirohisa Kishino, Shuichi Kitada
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.
read.genepop
# 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)
# Gst estimation
result.gstNC <- GstNC(popdata)
print(as.dist(result.gstNC))
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