DNAse_UCSC {coMET} | R Documentation

## Creation of an UCSC's DNase clusters track

### Description

Creation of DNase cluster track from a connection to UCSC genome browser in using the GViz bioconductor package

### Usage

    DNAse_UCSC(gen, chr, start, end, mySession, title="DNA cluster",
    track.name = "DNase Clusters", table.name = NULL)

### 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)
`mySession` | the object session from the function browserSession of rtracklayer
`title` | Name of tracks
`track.name` | the name of the track DNAse_UCSC. "DNase Clusters"(default)
`table.name` | the name of the table from the track

### Value

An AnnotationTrack 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=wgEncodeDNAseSuper

### Examples

    library("Gviz")
    library("rtracklayer")

    gen <- "hg19"
    chr <- "chr7"
    start <- 38290160
    end <- 38303219
    if(interactive()){
      BROWSER.SESSION="UCSC"
      mySession <- browserSession(BROWSER.SESSION)
      genome(mySession) <- gen
      track.name="Broad ChromHMM"
      tablestrack<-tableNames(ucscTableQuery(mySession, track=track.name))
      table.name<-tablestrack[1]
      dnasetrack<-DNAse_UCSC(gen,chr,start,end,mySession)
      plotTracks(dnasetrack, from = start, to =end)
    }else {
        data(dnasetrack)
       plotTracks(dnasetrack, from = start, to =end)
    }

[Package coMET version 1.12.0 Index]