gcContent_UCSC: Create one track of GC content from UCSC

Description Usage Arguments Value Author(s) References Examples

View source: R/BiofeatureGraphics.R

Description

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

Usage

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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

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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)
} else {
  data(gctrack)
  plotTracks(gctrack,from= start, to=end)
}

coMET documentation built on May 2, 2018, 4:21 a.m.