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

• Published in: Bioinformatics 2007-03, Vol.23 (6), p.774-776
• Main Authors: Luna, Augustin, Nicodemus, Kristin K.
• Format: Article
• Language: English
• Subjects: Algorithms; Biological and medical sciences; Chromosome Mapping - methods; Computer Graphics; DNA Mutational Analysis - methods; Fundamental and applied biological sciences. Psychology; General aspects; Haplotypes - genetics; Linkage Disequilibrium - genetics; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Polymorphism, Single Nucleotide - genetics; Programming Languages; Software; User-Computer Interface
• ISSN: 1367-4803; 1367-4811; 1460-2059
• DOI: 10.1093/bioinformatics/btl657

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: [e-mail]