Although genotyping arrays are most often used for calling genotypes, the raw data are quantitative measures of the binding of particular DNA variants. By pooling equal quantities of DNA from groups of people on the arrays, it is possible to calculate the relative frequency of alleles between cases and controls for a particular disease, or between the high and low extremes of a quantitative trait. The SNPMaP package for the R statistical computing environment provides a framework for this analysis, allowing genome-wide association studies using tens, rather than thousands of arrays.
SNPMaP is described in this Open Access article in the journal Bioinformatics:
Davis, O.S.P., Plomin, R., & Schalkwyk, L.C. (2009). The SNPMaP package for R: A framework for genome-wide association using DNA pooling on microarrays. Bioinformatics, 25, 281-283. doi:10.1093/bioinformatics/btn587
If you find the package useful for one of your studies, we'd be very grateful if you would cite the article.
SNPMaP is available on CRAN, but it requires the affxparser package from Bioconductor. You can install these packages through your usual GUI, or this script should do the trick. To use it, paste this at the R prompt:
|11.11.11||1.2.0||Better data compression, revised dependencies, namespace|
|17.09.10||1.1.0||Updates for new version of R|
|12.11.09||1.0.0||Initial release as an R package|
|0.9.0||SNPMaP available as a series of scripts|
If you have any comments or suggestions, or wish to report a bug, please get in touch (snpmap AT kcl.ac.uk)