Description Usage Arguments Details Value Examples

View source: R/calculate_fst.R

The FST value between two populations is calculated, given a number of markers. Markers are superimposed upon the (known) ancestry along the chromosome for all sampled individuals. Markers can be chosen to be regularly spaced, or randomly distributed.

1 2 | ```
calculate_fst(pop1, pop2, sampled_individuals, number_of_markers = 100,
random_markers = FALSE)
``` |

`pop1` |
Population object |

`pop2` |
Population object |

`sampled_individuals` |
Number of individuals to base the FST upon. Individuals are randomly drawn from each population, a lower number speeds up calculations. |

`number_of_markers` |
Number of markers along the chromosome used to calculate FST metrics. |

`random_markers` |
If TRUE, markers are randomly spaced along the chromosome, if FALSE, markers are equidistantly spaced along the chromosome. |

Uses the function `wc`

from the package `hierfstat`

to
calculate the FST. The function `wc`

computes the Weir and Cockerham
F statistic.

FST value

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ```
## Not run:
two_populations <- simulate_admixture_until(pop_size = 100,
number_of_founders = 20,
total_runtime = 10,
morgan = 1,
seed = 42,
overlap = 0.25)
FST <- calculate_fst(two_populations$Population_1,
two_populations$Population_2,
sampled_individuals = 10,
number_of_markers = 100,
random_markers = TRUE)
## End(Not run)
``` |

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