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Bioinformatics Advance Access originally published online on October 4, 2006
Bioinformatics 2006 22(24):3103-3105; doi:10.1093/bioinformatics/btl507
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

P2BAT: a massive parallel implementation of PBAT for genome-wide association studies in R

Thomas Hoffmann 1,* and Christoph Lange 1,2

1 Department of Biostatistics, Harvard School of Public Health 655 Huntington Avenue, Boston, MA 02115, USA
2 Harvard Medical School, Channing Laboratory 181 Longwood Avenue, Boston, MA 02115, USA

*To whom correpondence should be addressed.

Summary: The software tool P2BAT provides a massive parallel and user friendly implementation of the PBAT-analysis tools for family-based association tests (FBATs) in large-scale studies, including genome-wide association studies with several thousand subjects. Built on the original PBAT-implementation of the Lange–Van Steen algorithm to bypass the multiple testing problem in family-based association studies, P2BAT integrates all PBAT-analysis tools for binary and complex traits into R and makes them accessible through a user-friendly GUI. The genome-wide analysis tools are fully automated and can be ran massively parallel directly through the GUI. P2BAT is fully documented and contains graphical output tools for time-to-onset analysis. P2BAT also features the ability to test for gene and environment/drug interaction.

Availability: The P2BAT package is available as the R package ‘pbatR’ which can be downloaded from http://cran.r-project.org/. The PBAT-software is available at http://www.biostat.harvard.edu/~clange/.

Contact: thoffman{at}hsph.harvard.edu

Received on July 28, 2006; revised on September 8, 2006; accepted on September 28, 2006

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