A flexible tool to plot a genomic map for single nucleotide polymorphisms. Issue 1 (December 2016)

• Record Type: Journal Article
• Authors: Zhang, Fuquan
• Is Part Of: Source code for biology and medicine. Volume 11:Issue 1(2016)
• Page Start: 1
• Page End: 3
• Publication Date: 2016-12
• Subjects: R package -- Mapsnp -- SNP map; Biology -- Data processing -- Periodicals; Medicine -- Data processing -- Periodicals; Bioinformatics -- Periodicals; 570.285
• DOI: 10.1186/s13029-016-0052-z
• Languages: English
• ISSNs: 1751-0473

Abstract

Abstract Background Most 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. Results We 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. Conclusions The mapsnp package is a flexible software to visualize genomic map for SNPs, involving the relative chromosome location and the transcripts in the region.