Epistasis Blog

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

Saturday, May 07, 2005

MDR Analysis Module Update

With the Data Tool now finished (see May 3rd posting), we are turning our attention to the MDR Analysis module (v0.2.1). Here is a preview of the new features we are adding to the next release (v0.3):

1) Publication-quality figures of the multilocus MDR models.
2) The ability to save a snapshot of an MDR analysis so you can load it later.
3) A sign test to test the null hypothesis that number of testing accuracies with values > 0.5 (+)is equal to the number <= 0.5 (-) from 10 or 20 cross-validation intervals, for example. We think the sign test might be useful for deciding whether or not to proceed with a computationally expensive permutation test using the MDR Permutation Testing module. We don't see it being used for formal hypothesis testing unless the size and power of the test are determined to be acceptable.
4) The ability to save the raw results from the MDR analysis.
5) The ability to consider matched case-control or family-based data.

Here are a few features that are planned for future releases:

6) A progress bar.
7) The multilocus MDR model in the form of IF-THEN rules.
8) A command-line interface that can be used with scripting.
9) Threading to take advantage of multi-processor computers.
10) Wrapper-algorithms for variable/attribute selection.
11) Visualization of the fitness landscape.
12) Context-sensitive help.
13) Save results in XML format.

Is there something you would like to see added to MDR? Request it here.

More information about the open-source MDR software package including access to the JAVA source code and executables can be found here.

General information about the MDR method can be found here.

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