snpBiomart_ENSEMBL {coMET} | R Documentation

## Create a short variation track from ENSEMBL

### Description

Create a 'Short Variation' track from ENSEMBL using the Gviz bioconductor package

### Usage

    snpBiomart_ENSEMBL(gen,chr, start, end, dataset, showId=FALSE, title = "SNPs ENSEMBL")

### Arguments

`gen` | the name of the genome
`chr` | the chromosome of interest
`start` | the first position in the region of interest (the smallest value)
`end` | the last position in the region of interest (the largest value)
`dataset` | The name of the database. Example "hsapiens_snp_som"
`showId` | Show the the ID of element or not
`title` | The name of the annotation track

### Value

An AnnotationTrack object of Gviz

### Author(s)

Tiphaine Martin

### References

Go to ENSEMBL Biomart

http://bioconductor.org/packages/release/bioc/html/Gviz.html

### See Also

`snpLocations_UCSC`, `structureBiomart_ENSEMBL`, `COSMIC_UCSC`, `CoreillCNV_UCSC`, `ClinVarMain_UCSC`, `ClinVarCnv_UCSC`,

### Examples

    library("Gviz")
    gen <- "hg38"
    chr <- "chr2"
    start <- 38290160
    end <- 38303219

    if(interactive()){
      snptrack <- snpBiomart_ENSEMBL(gen,chr, start, end,
                           dataset="hsapiens_snp",showId=FALSE)
      plotTracks(snptrack, from=start, to=end)
    } else {
      data(snpBiomarttrack)
      plotTracks(snptrack, from=start, to=end)
    }

[Package coMET version 1.12.0 Index]