chromatinHMMAll_UCSC: Creating multiple chromHMM tracks from the UCSC genome browser

Description

Create multiple chromHMM Broad tracks by connecting to the UCSC genome browser using the GViz bioconductor package

Usage

chromatinHMMAll_UCSC(gen, chr, start, end, mySession, color='coMET',pattern = NULL, 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

color

the colour scheme used for plots. By defult this is set to 'coMET' to allow easy indentifcation of differnent elements. The colour scheme set by UCSC can also be used. Consult userguide for table of colours.

pattern

the pattern of the track to visualise

table.name

the name of the table from the track

Value

list of AnnotationTrack objects 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 <- 38313219
    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]
        PATTERN.REGULATION<-"GM12878"
        
        chromhmmPattern<-chromatinHMMAll_UCSC(gen,chr,start,end,mySession,color='coMET',PATTERN.REGULATION)
        plotTracks(chromhmmPattern, from = start, to =end)

        chromhmmNoPattern<-chromatinHMMAll_UCSC(gen,chr,start,end,mySession,color='coMET')
        plotTracks(chromhmmNoPattern, from = start, to =end)
    } else {

        data(chromhmmPattern)
        plotTracks(chromhmmPattern, from = start, to =end)

        data(chromhmmNoPattern)
        plotTracks(chromhmmNoPattern, from = start, to =end)
    }