chromatinHMMOne_UCSC {coMET} | R Documentation

## Creating one chromHMM track from the UCSC genome browser

### Description

Create one track of only one type of chromHMM Broad element from the UCSC genome browser using the Gviz bioconductor package

### Usage

    chromatinHMMOne_UCSC(gen, chr, start, end, mySession, color="coMET",
    title="ENCODE/Broad chromHMM", 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 region of interest (the smallest value)
`end` | the last position in region of interest (the biggest value)
`mySession` | the object session from the function browserSession of rtracklayer
`color` | the color scheme used for plots. By defult this is set to 'coMET' to allow easy indentifcation of differnent elements. The color scheme set by UCSC can also be used. Consult userguide for table of colors.
`title` | Name of tracks
`table.name` | the name of the table from the track

### Value

An AnnotationTrack object of Gviz

### Author(s)

Tiphaine Martin

Tom Hardiman

### References

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

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

### See Also

`chromatinHMMAll_UCSC`

### Examples

        library("Gviz")
        library("rtracklayer")
        gen <- "hg19"
        chr <- "chr2"
        start <- 38290160
        end <- 38303219
        color <- "coMET"

        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]
            chromhmmtrackone<-chromatinHMMOne_UCSC(gen,chr,start,end
            ,mySession,color="coMET",table.name)
            plotTracks(chromhmmtrackone, from = start, to =end)
        }else {
            data(chromhmmtrackone)
            plotTracks(chromhmmtrackone, from = start, to =end)
        }

[Package coMET version 1.16.0 Index]