refGenes_UCSC {coMET} | R Documentation

## Create a track of RefSeq genes from the UCSC genome browser

### Description

Create a track of RefSeq genes from the UCSC genome browser using the Gviz bioconductor package

### Usage

    refGenes_UCSC(gen, chr, start, end, title="Ref Genes UCSC", track = "refGene",
    IdType="Ref", showId=TRUE)

### 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)
`title` | Name of tracks
`track` | the name of table in UCSC for the group "Genes and Gene Prediction"
`IdType` | When set to 'ref' shows the gene reference, when set to "name" shows the gene name
`showId` | Shows the ID or name of the genetic elements

### Value

An UcscTrack object of Gviz

### Author(s)

Tiphaine Martin

Tom Hardiman

### References

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

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

### See Also

`ISCA_UCSC`, `GWAScatalog_UCSC`, `genesName_ENSEMBL`, `GeneReviews_UCSC`, `GAD_UCSC`, `genes_ENSEMBL`, `xenorefGenes_UCSC`, `transcript_ENSEMBL`, `knownGenes_UCSC`

### Examples

    library("Gviz")
    gen <- "hg38"
    chr <- "chr7"
    start <- 38203219
    end <- 38303219
    IdType <- "name"
    track <- "refGene"

    if(interactive()) {
      genesUcsctrack<-refGenes_UCSC(gen,chr,start,end,track,IdType)
      plotTracks(genesUcsctrack, from = start, to =end)
    }else {
      data(genesUcsctrack)
      plotTracks(genesUcsctrack, from = start, to =end)
    }

[Package coMET version 1.26.0 Index]