Version Compatibility

Reference examples tested with: LDpred2 1.14+, PRSice-2 2.3+, numpy 1.26+, scipy 1.12+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Polygenic Risk Scores

"Calculate polygenic risk scores for my cohort" → Compute genome-wide risk scores from GWAS summary statistics and individual genotypes to predict disease susceptibility.

• CLI: PRSice_linux --base gwas.txt --target genotypes --out prs_results
• R: bigsnpr::snp_ldpred2_auto() for LDpred2 Bayesian PRS

PRSice-2 Workflow