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

Zhang F, Xu Y, Cao H, Jin C, Cheng Z, Wang G, Shugart YY - PLoS ONE (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 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.

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.

No MeSH data available.


A genomic map for ATXN2 via Ensembl browser.
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pone.0123609.g004: A genomic map for ATXN2 via Ensembl browser.

Mentions: Since UCSC Genome Browser and Ensembl are two of the most commonly used genome visualization tools, we utilized these two browsers to illustrate the genomic information of ATXN2 gene. With UCSC browser, we input the ‘ATXN2’ and selected a subset tracks to show its genomic features (Fig 3). Next, we made a gene-based display for ATXN2 in Ensembl (Fig 4). As shown in Fig 3 and Fig 4, all of the common SNPs within ATXN2 were displayed. We could not select or highlight SNPs of interest within the gene. Fig 4 also lacks an ideogram track.


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

Zhang F, Xu Y, Cao H, Jin C, Cheng Z, Wang G, Shugart YY - PLoS ONE (2015)

A genomic map for ATXN2 via Ensembl browser.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390227&req=5

pone.0123609.g004: A genomic map for ATXN2 via Ensembl browser.
Mentions: Since UCSC Genome Browser and Ensembl are two of the most commonly used genome visualization tools, we utilized these two browsers to illustrate the genomic information of ATXN2 gene. With UCSC browser, we input the ‘ATXN2’ and selected a subset tracks to show its genomic features (Fig 3). Next, we made a gene-based display for ATXN2 in Ensembl (Fig 4). As shown in Fig 3 and Fig 4, all of the common SNPs within ATXN2 were displayed. We could not select or highlight SNPs of interest within the gene. Fig 4 also lacks an ideogram track.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 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.

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.

No MeSH data available.