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Bioinformatics Advance Access originally published online on November 12, 2008
Bioinformatics 2009 25(2):281-283; doi:10.1093/bioinformatics/btn587
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, De Crespigny Park, London SE5 8AF, UK

*To whom correspondence should be addressed.


  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{at}iop.kcl.ac.uk

Supplementary information: Additional resources and test datasets are available at http://sgdp.iop.kcl.ac.uk/snpmap/

Associate Editor: Martin Bishop

Received on July 14, 2008; revised on October 7, 2008; accepted on November 10, 2008

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