R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses.
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).


BACKGROUND
The package is freely available from cran.r-project.org.
Yandell
Brian S
BS
Department of Statistics, University of Wisconsin-Madison, 1300 University Avenue, Madison, WI 53706, USA. byandell@wisc.edu
Mehta
Tapan
T
Banerjee
Samprit
S
Shriner
Daniel
D
Venkataraman
Ramprasad
R
Moon
Jee Young
JY
Neely
W Whipple
WW
Wu
Hao
H
von Smith
Randy
R
Yi
Nengjun
N
D000465:Algorithms; D001499:Bayes Theorem; D002874:Chromosome Mapping; D003433:Crosses, Genetic; D004843:Epistasis, Genetic; D008390:Markov Chains; D009010:Monte Carlo Method; D040641:Quantitative Trait Loci