knownGenes_UCSC {coMET} | R Documentation

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

### Description

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

### Usage

    knownGenes_UCSC(gen, chr, start, end,title="UCSC known Genes", 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
`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=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`,

### Examples

    library("Gviz")
    gen <- "hg38"
    chr <- "chr7"
    start <- 38290160
    end <- 38303219

    if(interactive()) {
      genesUcsctrack<-knownGenes_UCSC(gen,chr,start,end,showId=TRUE)
      plotTracks(genesUcsctrack, from = start, to =end)
    }else {
      data(genesUcsctrack)
      plotTracks(genesUcsctrack, from = start, to =end)
    }

[Package coMET version 1.16.0 Index]