A brief tour of R/qtl

R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTLs) in experimental crosses. It is implemented as an add-on package for the freely available and widely used statistical language/software R (see www.r-project.org). The development of this software as an add-on to R allows us to take advantage of the basic mathematical and statistical functions, and powerful graphics capabilities, that are provided with R. Further, the user will benefit by the seamless integration of the QTL mapping software into a general statistical analysis program. Our goal is to make complex QTL mapping methods widely accessible and allow users to focus on modeling rather than computing. A key component of computational methods for QTL mapping is the hidden Markov model (HMM) technology for dealing with missing genotype data. We have implemented the main HMM algorithms, with allowance for the presence of genotyping errors, for backcrosses, intercrosses, and phase-known four-way crosses. The current version of R/qtl includes facilities for estimating genetic maps, identifying genotyping errors, and performing single-QTL genome scans and two-QTL, two-dimensional genome scans, by interval mapping (with the EM algorithm), HaleyKnott regression, and multiple imputation. All of this may be done in the presence of covariates (such as sex, age or treatment). The fit of higher-order QTL models, with sophisticated techniques for model comparison and model search, will be incorporated soon. R/qtl is distributed as source code for Unix or compiled code for Windows or Mac OS X. R/qtl is released under the GNU General Public License. To download the software, you must agree to the terms in that license.