chromatinHMMAll_UCSC: Creating multiple chromHMM tracks from the UCSC genome...

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

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

Author(s)

Tiphaine Martin

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

chromatinHMMOne_UCSC

Examples

    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)
    }

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