Description Usage Arguments Value Author(s) References See Also Examples
This function estimates pairwise Gst among subpopulations (Nei 1973) from a GENEPOP data object (Rousset 2008). Missing genotype values in the GENEPOP file ("0000" or "000000") are simply ignored.
1 | GstN(popdata)
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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 (1973) Analysis of Gene Diversity in Subdivided Populations. Proc. Nat. Acad. Sci., 70, 3321-3323.
Rousset F (2008) Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Resources, 8, 103-106.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | # 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.gstN <- GstN(popdata)
write.csv(result.gstN, "result_GstN.csv", na="")
print(as.dist(result.gstN))
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