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


BACKGROUND
Downloadable R package and example datasets are available at http://cbdb.nimh.nih.gov/~kristin/snp.plotter.html and http://www.r-project.org.
Luna
Augustin
A
GCAP/CBDB, NIMH/NIH, 10 Center Drive, Room 4S-235, Bethesda, MD 20814, USA.
Nicodemus
Kristin K
KK
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D003196:Computer Graphics; D004252:DNA Mutational Analysis / Q000379:methods*; D006239:Haplotypes / Q000235:genetics*; D015810:Linkage Disequilibrium / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011381:Programming Languages; D012984:Software; D014584:User-Computer Interface