Description Usage Arguments Value Examples

View source: R/calculate_tajima_d.R

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

1 2 | ```
calculate_tajima_d(pop, markers = seq(1e-06, 1 - 1e-06, length.out =
100), number_of_sampled_individuals = 10)
``` |

`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. |

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.

1 2 3 4 5 6 7 8 9 10 11 12 | ```
## 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/GenomeAdmixR documentation built on Oct. 20, 2019, 6:06 a.m.

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