calculate_marker_frequency: Calculate allele frequencies at a specific marker location

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

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.

Author(s)

Thijs Janzen

Examples

## Not run: 
  number_founders = 20
  wildpop =  create_population(pop_size = 1000,
                             number_of_founders = number_founders,
                             total_runtime = 10,
                             morgan = 1,
                             seed = 666)

  calculate_marker_frequency(wildpop, 0.5)
  frequencies <- calculate_marker_frequency(wildpop, seq(0.4, 0.5, by = 0.001))
  ggplot(frequencies, aes(x = location, y = frequency, col = ancestor)) +
      geom_step()


## End(Not run)

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