diversity_stats: Calculate Watterson's estimator of theta

In andrewparkermorgan/sfsr: Utilities for Manipulating Allele Frequency Spectra

Description

Calculate Watterson's estimator of theta

Calculate the Tajima's pi-hat estimator of theta (avg pairwise differences)

Calculate the Fu and Li's estimator of theta

Calculate the d_xy, the average pairwise divergence

Usage

theta_w(sfs, persite = FALSE, ...)

theta_pi(sfs, persite = FALSE, ...)

theta_zeta(sfs, persite = FALSE, ...)

d_xy(sfs, persite = FALSE, ...)

Arguments

sfs	an SFS
persite	logical; if TRUE, divide by number of sites
...	ignored

Value

Watterson's θ, the population-scaled mutation rate

value of \hat{π} = ∑_{i>j}^N{d_{ij}}, the average number of pairwise differences (aka expected heterozygosity)

value of \hat{θ_{ζ}}, the number of derived singletons in a sample

average pairwise divergence: if one population, to the outgroup (assuming unfolded, polarized SFS); if two populations, between them

References

Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-360.

Fu YX and Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133: 693-709.

andrewparkermorgan/sfsr documentation built on May 10, 2019, 11:10 a.m.