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. 2007 Mar 15;23(6):774-6.
doi: 10.1093/bioinformatics/btl657. Epub 2007 Jan 18.

snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package

Augustin Luna  1 , Kristin K Nicodemus
Affiliations

snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package

Augustin Luna et al. Bioinformatics. .

Abstract

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.

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