Optimisation of the core subset for the APY approximation of genomic relationships

Pocrnic, Lindgren, Tolhurst, Herring & Gorjanc (2022)

Published in GSE: Optimisation of the core subset for the APY approximation of genomic relationships

• functions.R includes (1) find_knots function to run conditional sampling core selection algorithms presented in the manuscript; (2) expand_B extension function; (3) APY_inverse brute force APY function (in the case you use free version of BLUPF90 that doesn't have OPTION apy ... available); (4) data_rec function to collect data from AlphaSimR simulation; (5) run_gblupf90 function to run BLUPF90 and read solutions into R; and (6) prepare_par function to prepare parameter file for BLUPF90.

• You might need to change the following line of code in functions.R based on your OS and location of the BLUPF90 binary;

system(command = "echo blupf90.par | $HOME/bin/blupf90 | tee blup.log"))

• OptimisedCore4APY.R includes the code to simulate the data using AlphaSimR and to generate core selection scenarios as in the manuscript.

• Please note that BLUPF90 program (Ignacy Misztal et al., University of Georgia, USA) has to be installed on your system. For download and installation details, please consult BLUPF90 website.