calculate_marker_frequency {GenomeAdmixR}

Calculate allele frequencies at a specific marker location

Description

Calculate the relative frequency of each ancestor in the population at a specific marker location

Usage

calculate_marker_frequency(pop, location)

Arguments

pop

Population for which to estimate allele frequencies at the given marker

location

A vector or scalar of location(s) along the chromosome for which allele frequencies are to be calculated. Locations are in Morgan.

Value

A tibble containing the frequency of each present ancestor at the provided location. Ancestors with frequency = 0 are dropped out of the table. The tibble contains three columns: location, ancestor and frequency.

Examples

wildpop =  simulate_admixture(
   module = ancestry_module(number_of_founders = 20, morgan = 1),
   pop_size = 1000,
   total_runtime = 10)

avg_frequencies <- calculate_marker_frequency(pop = wildpop,
                                              location = 0.5)

frequencies <-
   calculate_marker_frequency(pop = wildpop,
                              location = seq(0.4, 0.5, by = 0.01))
require(ggplot2)
ggplot(frequencies, aes(x = location, y = frequency, col = ancestor)) +
  geom_step()