The SNPMaP package for R: a framework for genome-wide association using DNA pooling on microarrays

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Abstract
Summary: Large-scale genome-wide association (GWA) studies using thousands of high-density SNP microarrays are becoming an essential tool in the search for loci related to heritable variation in many phenotypes. However, the cost of GWA remains beyond the reach of many researchers. Fortunately, the majority of statistical power can still be obtained by estimating allele frequencies from DNA pools, reducing the cost to that of tens, rather than thousands of arrays. We present a set of software tools for processing SNPMaP (SNP microarrays and pooling) data from CEL files to Relative Allele Scores in the rich R statistical computing environment. Availability: The SNPMaP package is available from http://cran.r-project.org/ under the GNU General Public License version 3 or later. Contact:snpmap@iop.kcl.ac.uk Supplementary information: Additional resources and test datasets are available at http://sgdp.iop.kcl.ac.uk/snpmap/