chromatinHMMAll_UCSC {coMET} | R Documentation

## 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

### 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)
        }

[Package coMET version 1.16.0 Index]