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

Augustin Luna, Kristin K Nicodemus

Research output: Contribution to journalArticlepeer-review

Abstract

UNLABELLED: 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.

Original languageEnglish
Pages (from-to)774-6
Number of pages3
JournalBioinformatics
Volume23
Issue number6
DOIs
Publication statusPublished - 15 Mar 2007

Keywords

  • Algorithms
  • Chromosome Mapping
  • Computer Graphics
  • DNA Mutational Analysis
  • Haplotypes
  • Linkage Disequilibrium
  • Polymorphism, Single Nucleotide
  • Programming Languages
  • Software
  • User-Computer Interface
  • Journal Article

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