COSMIC_UCSC {coMET} | R Documentation

## Create one track of the genomic positions of variants from COSMIC [obselete]

### Description

[obselete] No more possible to extract COSMIC data from UCSC.

Create one track of the genomic positions of variants from COSMIC, the "Catalogue Of Somatic Mutations In Cancer" in extracting data from UCSC and using the Gviz bioconductor package.

### Usage

    COSMIC_UCSC(gen, chr, start, end,title= "COSMIC", showId=FALSE)

### Arguments

`gen` | the name of the genome. Data is not currently available for GRCh38 (hg38)
`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)
`title` | The name of the annotation track
`showId` | Show the ID of the genetic elements

### Value

An UcscTrack object of Gviz

### Author(s)

Tiphaine Martin

### References

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

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=cosmic

### See Also

`snpLocations_UCSC`, `structureBiomart_ENSEMBL`, `snpBiomart_ENSEMBL`, `CoreillCNV_UCSC`, `ClinVarMain_UCSC`, `ClinVarCnv_UCSC`,

### Examples

    library("Gviz")
    chrom <- "chr2"
    start <- 38290160
    end <- 38303219
    gen <- "hg19"
    if(interactive()){
        cosmicVariant<-COSMIC_UCSC(gen,chrom,start,end)
        plotTracks(cosmicVariant, from = start, to =end)
    }else {
        data(cosmicVarianttrack)
        plotTracks(cosmicVariant, from = start, to =end)
    }

[Package coMET version 1.16.0 Index]