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Bioinformatics Advance Access originally published online on January 18, 2007
Bioinformatics 2007 23(6):774-776; 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,*

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

*To whom correspondence should be addressed.


  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 the 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/~kristin/snp.plotter.html and http://www.r-project.org

Contact: nicodemusk{at}mail.nih.gov

Associate Editor: Martin Bishop

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

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