gcContent_UCSC: Create one track of GC content from UCSC

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

Create one track of GC content from UCSC

Description

Create a track of GC content from UCSC using the Gviz bioconductor package

Usage

gcContent_UCSC(gen, chr, start, end, title="GC Percent")

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

A 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=gc5Base

Examples

library("Gviz")
gen <- "hg38"
chr <- "chr7"
start <- 38290160
end <- 38303219

if(interactive()){
  gctrack<-gcContent_UCSC(gen,chr,start,end)
  plotTracks(gctrack,from= start, to=end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(gctrack)
  plotTracks(gctrack,from= start, to=end,
                                   fontfamily="sans",fontfamily.title="sans")
}

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