chromatinHMMOne_UCSC: 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", 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.

table.name

the name of the table from the track

Value

An AnnotationTrack object of Gviz

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

Examples

Run this code

    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)
    }