ClinVarMain_UCSC {coMET} | R Documentation

## Create one track of the genomic positions of variants from the ClinVar database (variants only)

### Description

Create one track of the genomic positions of variants from the ClinVar database (Variants only, CNV excluded) using the Gviz bioconductor package

### Usage

    ClinVarMain_UCSC(gen, chr, start, end, title="ClinVar Variants", showId=FALSE)

### Arguments

`gen` | the name of the genome
`chr` | the chromosome of interest
`start` | the first position in region of interest (the smallest value)
`end` | the last position in region of interest (the biggest 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://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=clinvar

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

### See Also

`snpLocations_UCSC`, `structureBiomart_ENSEMBL`, `snpBiomart_ENSEMBL`, `CoreillCNV_UCSC`, `COSMIC_UCSC`, `ClinVarCnv_UCSC`

### Examples

    library("Gviz")
    gen <- "hg38"
    chrom <- "chr2"
    start <- 100000
    end <- 10000000

    if(interactive()) {
        clinVariant<-ClinVarMain_UCSC(gen,chrom,start,end)
        plotTracks(clinVariant, from = start, to =end)
    }else{
        data(clinVarMaintrack)
        plotTracks(clinVariant, from = start, to =end)
    }

[Package coMET version 1.16.0 Index]