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

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

Research output: Contribution to journal › Article › peer-review

4 Scopus citations

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 language	English (US)
Article number	e0123609
Journal	PLoS One
Volume	10
Issue number	4
DOIs	https://doi.org/10.1371/journal.pone.0123609
State	Published - Apr 8 2015
Externally published	Yes

ASJC Scopus subject areas

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

Access to Document

10.1371/journal.pone.0123609

Cite this

@article{d1b35ea5e7ab47ac896b145c8cc5df3d,

title = "Mapsnp: An R package to plot a genomic map for single nucleotide polymorphisms",

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.",

author = "Fuquan Zhang and Yong Xu and Hongbao Cao and Chunhui Jin and Zaohuo Cheng and Guoqiang Wang and Shugart, {Yin Yao}",

year = "2015",

month = apr,

day = "8",

doi = "10.1371/journal.pone.0123609",

language = "English (US)",

volume = "10",

journal = "PLoS One",

issn = "1932-6203",

publisher = "Public Library of Science",

number = "4",

}

TY - JOUR

T1 - Mapsnp

T2 - An R package to plot a genomic map for single nucleotide polymorphisms

AU - Zhang, Fuquan

AU - Xu, Yong

AU - Cao, Hongbao

AU - Jin, Chunhui

AU - Cheng, Zaohuo

AU - Wang, Guoqiang

AU - Shugart, Yin Yao

PY - 2015/4/8

Y1 - 2015/4/8

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84929497410&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84929497410&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0123609

DO - 10.1371/journal.pone.0123609

M3 - Article

C2 - 25853637

AN - SCOPUS:84929497410

SN - 1932-6203

VL - 10

JO - PLoS One

JF - PLoS One

IS - 4

M1 - e0123609

ER -

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

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this