calculate_fst: Calculate FST

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

Description

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.

Usage

calculate_fst(pop1, pop2,
        sampled_individuals, number_of_markers = 100, random_markers = FALSE)

Arguments

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.

Details

Uses the function wc from the package hierfstat to calculate the FST. The function wc computes the Weir and Cockerham F statistic.

Value

FST value

Author(s)

Thijs Janzen

Examples

## Not run: 
two_populations <- create_two_populations(pop_size = 1000,
                                          number_of_founders = 20,
                                          total_runtime = 100,
                                          morgan = 1,
                                          seed = 42,
                                          overlap = 0.25,
                                          write_to_file = FALSE)

  FST <- calculate_fst(two_populations$Population_1,
                 two_populations$Population_2,
                 sampled_individuals = 10,
                 number_of_markers = 100,
                 random_markers = TRUE)
  
## End(Not run)

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