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

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

Fuquan Zhang  1 , Yong Xu  2 , Hongbao Cao  3 , Chunhui Jin  4 , Zaohuo Cheng  4 , Guoqiang Wang  4 , Yin Yao Shugart  3
Affiliations

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

Fuquan Zhang et al. PLoS One. .

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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. A detailed genomic map for seven SNPs within ATXN2 using Ensembl database.
At the top, the relevant chromosome is drawn with the subregion of interest marked in red. The ‘Transcript’ track shows all the alternative transcripts within the region, retrieved from Ensembl database, including a non-ATXN2 transcript U7. At the bottom, the SNPs’ location and ID are plotted along the same genomic coordinate.
Fig 2
Fig 2. A concise genomic map for seven SNPs within ATXN2 using UCSC database.
At the top, the relevant chromosome is drawn with the subregion of interest marked in red. The ‘ATXN2’ track shows the combined gene model of the alternative transcripts of the ATXN2 gene. At the bottom, the SNPs’ location and ID are plotted along the same genomic coordinate. > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > msb(M = snp, start = 111950277, end = 112036294, geneTrName = ‘ATXN2’).
Fig 3
Fig 3. A genomic map for ATXN2 via UCSC browser.
Fig 4
Fig 4. A genomic map for ATXN2 via Ensembl browser.
See this image and copyright information in PMC

References

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