cpgIslands_UCSC: create track CpG Island from UCSC

Description Usage Arguments Value Author(s) References Examples

View source: R/BiofeatureGraphics.R

Description

create track CpG Island from UCSC using the Gviz bioconductor package

Usage

1

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

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

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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)
}

coMET documentation built on Nov. 23, 2017, 2:05 a.m.