CoreillCNV_UCSC {coMET} | R Documentation

## Create one track of the genomic positions of CNV in chromosomal aberration and inherited disorders from the NIGMS Human Genetic Cell Repository data

### Description

Create one track of the genomic positions of copy-number variants (CNVs) in chromosomal aberration and inherited disorder cell lines from the NIGMS Human Genetic Cell Repository using the Gviz bioconductor package.

### Usage

    CoreillCNV_UCSC(gen, chr, start, end,title="Coriell CNVs", 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=coriellDelDup

### See Also

`snpLocations_UCSC`, `structureBiomart_ENSEMBL`, `snpBiomart_ENSEMBL`, `COSMIC_UCSC`, `ClinVarMain_UCSC`, `ClinVarCnv_UCSC`

### Examples

    library("Gviz")
    gen <- "hg19"
    chrom <- "chr2"
    start <- 38290160
    end <- 38303219

    if(interactive()){
        coreilVariant<-CoreillCNV_UCSC(gen,chrom,start,end)
        plotTracks(coreilVariant, from = start, to =end)
    } else {
         data(coreilVarianttrack)
        plotTracks(coreilVariant, from = start, to =end)
    }

[Package coMET version 1.16.0 Index]