calculate_tajima_d: Calculate Tajima's d

In thijsjanzen/isoSIM: Simulate Linkage Disequilibrium Along Chromosomes in Isofemale Lines

Description

Tajima's d is calculated, given a number of markers.

Usage

calculate_tajima_d(pop,
                   markers = seq(1e-6,1-1e-6,length.out = 100),
                   number_of_sampled_individuals = 10)

Arguments

pop	Population object
markers	Vector from 0 to 1 (excluding 0 and 1) indicating the locations of the markers used for the analysis
number_of_sampled_individuals	Number of individuals to base Tajima's d upon. Individuals are randomly drawn from the population.

Value

A list with the following entries: D Tajima's D, pi pi, the average pairwise differences across the number of selected markers. S the number of segregating sites and theta_hat, the expected value of pi, calculated from S, such that theta = S/a1.

Author(s)

Thijs Janzen

Examples

## Not run: 
pop <- simulate_admixture(pop_size = 100,
                          number_of_founders = 2,
                          total_runtime = 100,
                          seed = 42)$population

calculate_tajima_d(pop,
                   markers = seq(1e-6,1-1e-6,100)),
                   number_of_sampled_individuals = 10)


## End(Not run)

thijsjanzen/isoSIM documentation built on May 29, 2019, 10:39 a.m.