Epistasis Blog

From the Computational Genetics Laboratory at the University of Pennsylvania (www.epistasis.org)

Saturday, October 02, 2010

Random Jungles

This is the latest in a series of paper developing random forest methods for the analysis of high-dimensional data. Note the software is freely available. http://www.randomjungle.org

Schwarz DF, K├Ânig IR, Ziegler A. On safari to Random Jungle: a fast implementation of Random Forests for high-dimensional data. Bioinformatics. 2010 Jul 15;26(14):1752-8. [PubMed]


MOTIVATION: Genome-wide association (GWA) studies have proven to be a successful approach for helping unravel the genetic basis of complex genetic diseases. However, the identified associations are not well suited for disease prediction, and only a modest portion of the heritability can be explained for most diseases, such as Type 2 diabetes or Crohn's disease. This may partly be due to the low power of standard statistical approaches to detect gene-gene and gene-environment interactions when small marginal effects are present. A promising alternative is Random Forests, which have already been successfully applied in candidate gene analyses. Important single nucleotide polymorphisms are detected by permutation importance measures. To this day, the application to GWA data was highly cumbersome with existing implementations because of the high computational burden.

RESULTS: Here, we present the new freely available software package Random Jungle (RJ), which facilitates the rapid analysis of GWA data. The program yields valid results and computes up to 159 times faster than the fastest alternative implementation, while still maintaining all options of other programs. Specifically, it offers the different permutation importance measures available. It includes new options such as the backward elimination method. We illustrate the application of RJ to a GWA of Crohn's disease. The most important single nucleotide polymorphisms (SNPs) validate recent findings in the literature and reveal potential interactions.

AVAILABILITY: The RJ software package is freely available at http://www.randomjungle.org


At 11:35 PM, Blogger hexhead said...

Jason, I am working with this software now. The main web site has gone and the project pulled back into the lab in Germany. Binaries are still available, but using the package as a library requires some reverse engineering. Works well, but I thought I'd share my experience if people are thinking of linking to the C++ library.


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