DAPath is a disease associated path analysis tool for discovering signaling paths and the pathways that contain these paths which are subjected to cumulative impact of modestly associated variants.
DAPath uses KEGG pathways and gene-p value pairings in your local directory to find affected paths in KEGG pathways. A path is composed of an input node, an output node, and the intermediate nodes that constitute the path in-between. If there are alternatives in-between, each is accepted as a distinct path.
It is better to remove metabolism pathways from your KEGG folder when they are irrelevant as they are highly connected and create too many alternative paths.
Code and sample files are available in
Related paper is available at [https://www.biorxiv.org/content/early/2018/05/08/316562]
Ozisik, O., Meguro, A., Mizuki, N., Diri, B., Sezerman, O.U., (2018), "A Scoring System to Evaluate the Impact of SNPs in a Path Related Context to Study Behcet's Disease Aetiology in Japanese Population", bioRxiv 316562, DOI:10.1101/316562