chromatinHMMOne: 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(gen, chr, start, end, mySession, track.name = "Broad ChromHMM",  table.name = NULL)

Arguments

gen

the name of the genome

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

track.name

the name of the track( Broad ChromHMM )

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")
    gen <- "hg19"
    chr <- "chr2"
    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]
        chromhmmtrackone<-chromatinHMMOne(gen,chr,start,end,mySession,track.name,table.name)
        plotTracks(chromhmmtrackone, from = start, to =end) 
    }else {
        data(chromhmmtrackone)
        plotTracks(chromhmmtrackone, from = start, to =end) 
    }