PoDA is a pathway-based, multi-SNP analysis method for GWAS data based upon the hypothesis that if a pathway is related to disease risk, cases will appear more similar to other cases than to controls for the SNPs associated with that pathway. PoDA improves on existing single-SNP and SNP-set enrichment analyses in that it does not require the SNPs in a pathway to exhibit independent main effects, making it an effective method even when epistasis is present.
Code:
- PoDA.R – Main script to perform the PoDA calculations
- PoDA-example.R – Example usage of PoDA.R
- PoDA-example-data.RData – Data used in PoDA-example.R (necessary for example)
- plotSvals.R – A script to generate the boxplots of the S values, similar to those shown in the paper.
