calculate_allele_frequencies: Calculate allele frequencies

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

Description

Calculate for a number of regularly spaced markers the relative frequency of each ancestor in the population.

Usage

calculate_allele_frequencies(source_pop, step_size, progress_bar)

Arguments

source_pop	Population for which to estimate allele frequencies
step_size	Distance between markers, a smaller step_size provides a more complete overview, but is also more computationally heavy.
progress_bar	Displays a progress_bar if TRUE. Default value is TRUE

Details

Markers are equidistantly spaced, with a distance of step_size in between them.

Value

A tibble containing the allele frequencies

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)

 freq_output <- calculate_allele_frequencies(wildpop,
                                            step_size = 0.001,
                                            progress_bar = TRUE)

  require(ggplot2)
  ggplot(freq_output, aes(x=location, y = frequency, col = as.factor(ancestor))) +
    geom_line()

## End(Not run)

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