cpgIslands_UCSC: create track CpG Island from UCSC

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

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,
    fontfamily="sans",fontfamily.title="sans")
}else {
    data(cpgIslandtrack)
    plotTracks(cpgIstrack, from = start, to =end,
    fontfamily="sans",fontfamily.title="sans")
}

TiphaineCMartin/coMET documentation built on April 27, 2022, 6:45 a.m.