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Bioinformatics Advance Access published online on October 4, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl507
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© 2006 The Author(s)
Received July 28, 2006
Revised September 8, 2006
Accepted September 28, 2006

Applications note

P2BAT: A Massive Parallel Implementation of PBAT for Genome-Wide Association Studies in R

Thomas Hoffmann 1 * and Christoph Lange 2

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

* To whom correspondence should be addressed.
Thomas Hoffmann, E-mail: thoffman{at}hsph.harvard.edu


  Abstract

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-VanSteen algorithm [9, 14] 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/.

Associate Editor: Keith A Crandall
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