Version Compatibility

Reference examples tested with: matplotlib 3.8+, numpy 1.26+, pandas 2.2+, 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
• 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.

Association Testing

"Run a GWAS on my genotyping data" → Perform genome-wide association testing using logistic (case-control) or linear (quantitative) regression with covariates, then visualize results with Manhattan and QQ plots.

• CLI: plink2 --glm for association testing with covariates

GWAS analysis using PLINK 2.0's unified --glm command for case-control and quantitative traits.

PLINK 2.0 Association Testing