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

doi:10.1371/journal.pone.0123609

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

PLoS One. 2015 Apr 8;10(4):e0123609. doi: 10.1371/journal.pone.0123609. eCollection 2015.

Authors

Fuquan Zhang¹, Yong Xu², Hongbao Cao³, Chunhui Jin⁴, Zaohuo Cheng⁴, Guoqiang Wang⁴, Yin Yao Shugart³

Affiliations

¹ Wuxi Mental Health Center of Nanjing Medical University, Wuxi, Jiangsu Province, China; Unit on Statistical Genomics, Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, United States of America.
² Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, China.
³ Unit on Statistical Genomics, Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, United States of America.
⁴ Wuxi Mental Health Center of Nanjing Medical University, Wuxi, Jiangsu Province, China.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Ataxin-2 / genetics
Chromosome Mapping / methods*
Humans
Polymorphism, Single Nucleotide*
Software*

Substances

ATXN2 protein, human
Ataxin-2

Grants and funding

This work was supported by Wuxi Hospital Management Center key joint scientific and technical project in medicine (YGZXL1315), the National Natural Science Foundation of China (81000583, 81278412), China Postdoctoral Science Foundation (2013M541207), Program for New Century Excellent Talents in University (YX), and Program for the Top Young Academic Leaders of Higher Learning Institutions of Shanxi (YX). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.