structureBiomart_ENSEMBL {coMET} | R Documentation

## Create a structural variation track from ENSEMBL

### Description

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

### Usage

    structureBiomart_ENSEMBL(gen, chr, start, end, strand, dataset,
    showId=FALSE, title = "Structural variation")

### 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)
`strand` | the strand to extract structure data for
`dataset` | The name of the database. Example "hsapiens_structvar_som"
`showId` | Show the the ID of the element
`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`, `snpBiomart_ENSEMBL`, `COSMIC_UCSC`, `CoreillCNV_UCSC`, `ClinVarMain_UCSC`, `ClinVarCnv_UCSC`,

### Examples

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

    if(interactive()){
      strutrack <- structureBiomart_ENSEMBL(chr, start, end,
                                  strand, dataset="hsapiens_structvar_som")
      plotTracks(strutrack, from=start, to=end)
    }else {
      data(strucBiomarttrack)
      plotTracks(strutrack, from=start, to=end)
    }

[Package coMET version 1.26.0 Index]