Epistasis Blog

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

Monday, September 05, 2011

An R Package Implementation of Multifactor Dimensionality Reduction

A new R package for our Multifactor Dimensionality Reduction (MDR) method is available.

Winham SJ, Motsinger-Reif AA. An R Package Implementation of Multifactor Dimensionality Reduction. BioData Min. 2011 Aug 16;4(1):24. [PubMed]

ABSTRACT:

BACKGROUND:

A breadth of high-dimensional data is now available with unprecedented numbers of genetic markers and data-mining approaches to variable selection are increasingly being utilized to uncover associations, including potential gene-gene and gene-environment interactions. One of the most commonly used data-mining methods for case-control data is Multifactor Dimensionality Reduction (MDR), which has displayed success in both simulations and real data applications. Additional software applications in alternative programming languages can improve the availability and usefulness of the method for a broader range of users.

RESULTS:

We introduce a package for the R statistical language to implement the Multifactor Dimensionality Reduction (MDR) method for nonparametric variable selection of interactions. This package is designed to provide an alternative implementation for R users, with great flexibility and utility for both data analysis and research. The 'MDR' package is freely available online at http://www.r-project.org/. We also provide data examples to illustrate the use and functionality of the package.

CONCLUSIONS:

MDR is a frequently-used data-mining method to identify potential gene-gene interactions, and alternative implementations will further increase this usage. We introduce a flexible software package for R users.

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