Statistics software packages and relational database systems possess considerable overlap in the area of data loading, handling, and transformation. However, only databases are mainly optimized towards high performance in this area. In this paper, we present our approach on bringing the best of these two worlds together. We integrate the analytics-optimized database MonetDB and the R environment for statistical computing in a non-obtrusive, transparent and compatible way.

Abstract Summary: GWASTools is an R/Bioconductor package for quality control and analysis of genome-wide association studies (GWAS). GWASTools brings the interactive capability and extensive statistical libraries of R to GWAS. Data are stored in NetCDF format to accommodate extremely large datasets that cannot fit within R’s memory limits. The documentation includes instructions for converting data from multiple formats, including variants called from sequencing. GWASTools provides a convenient interface for linking genotypes and intensity data with sample and single nucleotide polymorphism annotation. Availability and implementation: GWASTools is implemented in R and is available from Bioconductor (http://www.bioconductor.org). An extensive vignette detailing a recommended work flow is included. Contact: [email protected]

MOTIVATION: Statistical analyses of genome-wide association studies (GWAS) require fitting large numbers of very similar regression models, each with low statistical power. Taking advantage of repeated observations or correlated phenotypes can increase this statistical power, but fitting the more complicated models required can make computation impractical. RESULTS: In this article, we present simple methods that capitalize on the structure inherent in GWAS studies to dramatically speed up computation for a wide variety of problems, with a special focus on methods for correlated phenotypes. AVAILABILITY: The R package 'boss' is available on the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/web/packages/boss/