Mapsnp: An R package to plot a genomic map for single nucleotide polymorphisms

Fuquan Zhang, Yong Xu, Hongbao Cao, Chunhui Jin, Zaohuo Cheng, Guoqiang Wang, Yin Yao Shugart

Research output: Contribution to journalArticle

Abstract

Single-nucleotide polymorphism (SNP) is one of the most common sources of genetic variations of the genome. Currently, SNPs are a main target for most genetic association studies. Visualizing genomic coordinates of SNPs, including their physical location relative to their host gene, and the structure of the relevant transcripts, may provide intuitive supplements to the understanding of their functions. Nevertheless, to date, no such easy-to-use programming tools exist. Therefore, we developed an R package, "mapsnp", to plot genomic map for a panel of SNPs within a genome region of interest, including the relative chromosome location and the transcripts in the region. mapsnp is a simple and flexible software package which can be used to visualize a genomic map for SNPs, integrating a chromosome ideogram, genomic coordinates, SNP locations and SNP labels.

Original languageEnglish (US)
Article numbere0123609
JournalPLoS One
Volume10
Issue number4
DOIs
StatePublished - Apr 8 2015
Externally publishedYes

    Fingerprint

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Zhang, F., Xu, Y., Cao, H., Jin, C., Cheng, Z., Wang, G., & Shugart, Y. Y. (2015). Mapsnp: An R package to plot a genomic map for single nucleotide polymorphisms. PLoS One, 10(4), [e0123609]. https://doi.org/10.1371/journal.pone.0123609