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Bioinformatics Advance Access published online on January 18, 2007
Bioinformatics, doi:10.1093/bioinformatics/btl657
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

snp.plotter: An R based SNP/Haplotype Association and Linkage Disequilibrium Plotting Package

Augustin Luna 1 and Kristin K. Nicodemus 1,2,*

1GCAP/CBDB, NIH/NIMH, 10 Center Drive; Room 4S-235, Bethesda, MD 20814,
2Epidemiology, Johns Hopkins SPH, Baltimore, MD

*To whom correspondence should be addressed. Kristin K. Nicodemus, Email: nicodemusk{at}mail.nih.gov


  Abstract

Summary: snp.plotter is a newly-developed R package which produces high-quality plots of results from genetic association studies. The main features of the package include options to display a linkage disequilibrium (LD) plot below a p-value plot using either the r2 or D' LD metric, to set the X-axis to equal spacing or to use the physical map of markers and to specify plot labels, colors, symbols and LD heatmap color scheme. snp.plotter can plot single SNP and/or haplotype data and simultaneously plot multiple sets of results. R is a free software environment for statistical computing and graphics available for most platforms. The proposed package provides a simple way to convey both association and LD information in a single appealing graphic for genetic association studies.

Availability: Downloadable R package and example datasets are available at http://cbdb.nimh.nih.gov/%7Ekristin/snp.plotter.html

Associate Editor: Martin Bishop

Received on November 21, 2006; revised on November 21, 2006; accepted on December 21, 2006

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