The effect of recombination rate on genomic selection in simulation

This repository contains code underlying the conference contribution:

M. Johnsson, A.M. Johansson, T. Klingström and E. Rius-Vilarrasa (2022) "The effect of recombination rate on genomic selection in simulation" Submitted to WCGALP 2022.

Simulations with variable recombination rate

The main contents is a simulation using AlphaSimR with real published linkage maps from cattle and chickens.

• R/simulation_functions.R -- helper functions for the AlphaSimR simulation

• R/simulate_chromosome_length.R -- simulation with variable chromosome length but uniform recombination rate

• R/simulate_karyotype.R -- simulation with real chromsome lengths but uniform recombination rate

• R/simulate_real_map.R -- simulation with real linkage maps

Preparataion of maps

• R/make_cattle_genome_table.R and R/make_chicken_genome_table.R process linkage maps and physical maps for simulation

• R/plot_map_difference.R illustrates the adjustment of simulated maps to real maps

Linkage equilibrium simulation

For comparison, we run a simulation with similar genetic parameters but genotypes are drawn independently each generation.

• R/simulation_functions_linkage_equilibrium.R -- helper functions for LE simulation

• R/simulate_linkage_equilibrium.R -- run LE simulation

Bash scripts to run

The scripts directory contains bash scripts to run replicates of the simulations with different parameters.

Summaries of results

• R/summarise_results.R and R/summarise_results_linkage_equilibrium.R summarises simulation runs and puts statistics in the outputs directory.

• R/plot_results.R contains plotting code