PoDA is a pathway-based, multi-SNP analysis method for GWAS data. The method is 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; by systematically applying the method to all pathways of potential interest, we can identify those for which the hypothesis holds true, i.e., pathways containing SNPs for which the samples exhibit greater within-class similarity than across classes. 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.
An R package to carry out the PoDA analysis will be available here in the near future (It will also be made available on BioConductor at that time).
In the meantime, a simple R script to carry out PoDA is available:
Please note that this is a bare-bones implementation and will be replaced by a full-featured R package. The code and data is provided without warrantee.
Please email Rosemary Braun at rosemary.braun_AT_GMAIL_DOT_COM if you have any questions, concerns, or feedback!