Journal Article

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

Oliver S. P. Davis, Robert Plomin and Leonard C. Schalkwyk

in Bioinformatics

Volume 25, issue 2, pages 281-283
Published in print January 2009 | ISSN: 1367-4803
Published online September 2008 | e-ISSN: 1460-2059 | DOI:

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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 under the GNU General Public License version 3 or later.


Supplementary information: Additional resources and test datasets are available at

Journal Article.  2012 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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