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Bioinformatics Advance Access first published online on January 19, 2007
This version published online on January 22, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm011
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

R/qtlbim: QTL with Bayesian Interval Mapping in Experimental Crosses

Brian S. Yandell 1,2,*, Tapan Mehta 3, Samprit Banerjee 3, Daniel Shriner 3, Ramprasad Venkataraman 3, Jee Young Moon 1, W. Whipple Neely 1, Hao Wu 4, Randy von Smith 5 and Nengjun Yi 3

1Department of Statistics, University of Wisconsin-Madison, 1300 University Avenue, Madison, WI 53706, USA; 2Department of Horticulture, University of Wisconsin-Madison, 1300 University Avenue, Madison, WI 53706, USA; 3Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; 4Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205 USA; and 5The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA.

*To whom correspondence should be addressed. Brian S. Yandell, E-mail: byandell{at}wisc.edu or nyi{at}ms.soph.uab.edu


  Abstract

Summary: R/qtlbim is an extensible, interactive environment for the Bayesian Interval Mapping of QTL, built on top of R/qtl (Broman et al. 2003), providing Bayesian analysis of multiple interacting quantitative trait loci (QTL) models for continuous, binary and ordinal traits in experimental crosses. It includes several efficient Markov chain Monte Carlo (MCMC) algorithms for evaluating the posterior of genetic architectures, i.e. the number and locations of QTL, their main and epistatic effects, and gene-environment interactions. R/qtlbim provides extensive informative graphical and numerical summaries, and model selection and convergence diagnostics of the MCMC output, illustrated through the vignette, example and demo capabilities of R (R Development Core Team 2006).

Availability: The package is freely available from cran.r-project.org.

Associate Editor: Keith Crandall

Received on October 25, 2006; revised on December 11, 2006; accepted on January 12, 2007

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