Description Usage Arguments Details Value References See Also Examples
Returns Fu's Fs statistic.
1 | hfufs(n, k, theta)
|
n |
The number of total sequences/individuals |
k |
The number of unique alleles |
theta |
The average pairwise nucleotide divergence |
Fu's Fs is a population genetics statistic that is useful for detecting loci that are responsible for population expansion, for example. Fu's Fs can be formulated as a calculation that involves Stirling numbers of the first kind. These can get large very quickly and exceed the floating point range for modern genomic data sets.
‘hfufs' calculates Fu’s Fs either directly, if the numbers are small enough, or using a logarithmic estimator for Stirling numbers implemented in the lstirling function.
Fu's Fs
Fu, Y.X. (1997) Statistical Tests of Neutrality of Mutations Against Population Growth, Hitchhiking and Background Selection. Genetics 147:915-25
‘hstrobecks' for a Strobeck’s S calculator and 'lstirling' for the Stirling number estimator
1 2 3 4 5 | n <- 100
k <- 30
theta <- 12.345
hfufs(n, k, theta)
# -0.7374915
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