cpgIslands_UCSC {coMET} | R Documentation

## create track CpG Island from UCSC

### Description

create track CpG Island from UCSC using the Gviz bioconductor package

### Usage

    cpgIslands_UCSC(gen, chr, start, end, title="CpG Islands UCSC")

### Arguments

`gen` | the name of the genome
`chr` | the chromosome of interest
`start` | the first position in the region of interest (the smallest value)
`end` | the last position in the region of interest (the largest value)
`title` | Name of tracks

### Value

An UcscTrack object 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=cpgIslandSuper

### Examples

    library("Gviz")
    chrom <- "chr2"
    start <- 100000
    end <- 1000000
    gen <- "hg38"

    if(interactive()) {
        cpgIstrack<-cpgIslands_UCSC(gen, chrom, start, end)
        plotTracks(cpgIstrack, from = start, to =end)
    }else {
        data(cpgIslandtrack)
        plotTracks(cpgIstrack, from = start, to =end)
    }

[Package coMET version 1.12.0 Index]