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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 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’).
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pone.0123609.g002: 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’).

Mentions: To circumvent the above issue, we created another function, msb, which leverages existent UCSC dataset curated by the ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ package for the construction of a transcript track. It contains only the major transcripts within the genomic region. Thus, multiple transcripts can be safely merged together to produce a concise genomic map. The following commands will load the dataset and plot a genomic map for the ATXN2 SNPs, with only one merged transcript (Fig 2).


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 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’).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0123609.g002: 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’).
Mentions: To circumvent the above issue, we created another function, msb, which leverages existent UCSC dataset curated by the ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ package for the construction of a transcript track. It contains only the major transcripts within the genomic region. Thus, multiple transcripts can be safely merged together to produce a concise genomic map. The following commands will load the dataset and plot a genomic map for the ATXN2 SNPs, with only one merged transcript (Fig 2).

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.