The *ABEL suite of R packages and software for genetic analysis has grown substantially since the appearance of GenABEL and the previously mentioned ProbABEL R packages. There are now a handful of useful R packages and other software utilities facilitating genome-wide association studies, analysis of imputed data, meta-analysis, efficient data storage, prediction, parallelization, and mixed model methods. The new GenABEL website also has prominent links to extensive documentation in manuals and tutorials. Finally, there's a new forum you can visit if you can't find an answer in the manuals or tutorials.
The GenABEL Project for Statistical Genetics Analysis