chromatinHMMOne_UCSC: Creating one chromHMM track from the UCSC genome browser

In TiphaineCMartin/coMET_original: coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.

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

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)
    }

TiphaineCMartin/coMET_original documentation built on May 9, 2019, 4:49 p.m.