coMET (version 1.4.4)

segmentalDups_UCSC: Create one track of the genomic positions of regions from segmentalDups_UCSC

Description

Create one track of the genomic positions of regions from segmentalDups_UCSC using the Gviz bioconductor package

Usage

segmentalDups_UCSC(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=rmsk

Examples

library("Gviz")
gen <- "hg38"
chr <- "chr2"
start <- 100000
end <- 200000

if(interactive()){
  DupTrack <-segmentalDups_UCSC(gen,chr,start,end)
  plotTracks(DupTrack, from = start, to = end)
} else {
  data(DupTrack)
  plotTracks(DupTrack, from = start, to = end)
}