I'm conducting a simulation and I need to obtain polygenic risk scores (PRS) using genome wide association studies (GWAS) summary statistics. It is known that the GWAS will give BETA and OR for quantitative and binary phenotypes respectively. When conducting the simulation for quantitative traits I used the following code to obtain PRS from GWAS performed:
./plink1.9 --bfile binary_file1_name --linear interaction --pheno pheno_file_name --covar cov_file_name --parameters 1 --allow-no-sex
./plink1.9 --bfile binary_file2_name --score plink.assoc.linear 2 4 7 header --out prs_quantitative
This is fine, where plink.assoc.linear file contains BETA.
When conducting simulation for binary traits I used the following code to obtain PRS from GWAS performed:
./plink1.9 --bfile binary_file1_name --logistic interaction --pheno pheno_file_name --covar cov_file_name --parameters 1 --allow-no-sex
./plink1.9 --bfile binary_file2_name --score plink.assoc.logistic 2 4 7 header --out prs_binary
I'm not sure whether we need to transform OR to BETA before inputting the file to --score in performing this for binary traits or, simply use the original plink.assoc.logistic which has OR (instead of BETA) to go ahead.
Simply, do we need to input file containing BETA values "only" for --score or either a file containing OR values or BETA values is fine?
