coMET (version 1.2.0)

cpgIslandsUCSC: create track CpG Island from UCSC

Description

create track CpG Island from UCSC using the Gviz bioconductor package

Usage

cpgIslandsUCSC(gen, chr, start, end)

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)

Value

An UcscTrack 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=cpgIslandSuper

Examples

library("Gviz")
chrom <- "chr2"
start <- 38290160
end <- 38303219
gen <- "hg19"

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