GenomeAdmixR (version 2.1.7)

iso_female_sequence: Create isofemale

Description

Creates isofemale individuals, given a population

Usage

iso_female_sequence(
  input_data = NA,
  n = 1,
  inbreeding_pop_size = 100,
  run_time = 2000,
  morgan = 1,
  recombination_rate = NA,
  num_threads = 1,
  verbose = FALSE
)

Arguments

input_data

Source population from which isofemales are generated

n

Number of isofemales to be generated

inbreeding_pop_size

Population size of the population used to generate homozygous individuals

run_time

Maximum runtime used for inbreeding

morgan

Size of the chromosome in Morgan (e.g. the number of crossovers during meiosis)

recombination_rate

rate in cM / Mbp, used to map recombination to the markers. If the recombination_rate is not set, the value for Morgan is used, assuming that the markers included span an entire chromosome.

num_threads

number of threads. Default is 1. Set to -1 to use all available threads

verbose

Displays verbose output if TRUE. Default value is FALSE

Value

A list of length n, where each entry is a fully homozygous isofemale.

Details

To create an isofemale, two individuals are randomly picked from the source population. Using these two individuals, a new population is seeded, of size inbreeding_pop_size. Then, this population is allowed to inbreed until either run_time is reached, or until all individuals are homozygous and genetically identical, whatever happens first.