Abstract
BackgroundMost genetic association studies use single-nucleotide polymorphisms (SNPs) as the research targets. However, resources to visualize the genomic map of candidate SNPs in a programming manner are limited. We have previously created an R package, mapsnp v0.1, to plot the genomic map for a panel of SNPs within a genomic region of interest. It failed to work under the latest version of Gviz package.ResultsWe updated the mapsnp package to keep up with the latest package environment and improved its functionality by adding more parameters to fine tune plotting outputs.ConclusionsThe mapsnp package is a flexible software to visualize genomic map for SNPs, involving the relative chromosome location and the transcripts in the region.Electronic supplementary materialThe online version of this article (doi:10.1186/s13029-016-0052-z) contains supplementary material, which is available to authorized users.
Highlights
Most genetic association studies use single-nucleotide polymorphisms (SNPs) as the research targets
We have developed mapsnp v0.1 [8] to plot genomic maps for SNPs
Implementation The mapsnp package leverages the Gviz system [7] to plot a genomic map for SNPs
Summary
Most genetic association studies use single-nucleotide polymorphisms (SNPs) as the research targets. Visualizing genomic map relevant to SNPs may inform the reader intuitively. UCSC and Ensembl Browser offers a set of annotation ‘tracks’ for a genomic region.
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