PoDA

Pathways of Distinction Analysis

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.

• For information about the method, please read:
  Rosemary Braun and Ken Buetow. Pathways of Distinction Analysis: A New Technique for Multi-SNP Analysis of GWAS Data. PLoS Genetics, 7(6):e1002101 (2011).

R code

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:

• 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.

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.

Credits

• Authors:
  Rosemary Braun and Ken Buetow
  Laboratory of Population Genetics
  National Cancer Institute, National Institutes of Health
• If you use or modify the code, please cite:
  Rosemary Braun and Ken Buetow. Pathways of Distinction Analysis: A New Technique for Multi-SNP Analysis of GWAS Data. PLoS Genetics, 7(6):e1002101 (2011).

Issues?

Please email Rosemary Braun at rosemary.braun_AT_GMAIL_DOT_COM if you have any questions, concerns, or feedback!