Description Usage Arguments Details Value Author(s) Examples
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
Thijs Janzen
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## 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)
|
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