coMET (version 1.4.4)

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

Description

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

Usage

repeatMasker_UCSC(gen, chr, start, end, showId=FALSE,type_stacking="full")

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)

showId

Show the ID of the genetic elements

type_stacking

the type of stacking data for this track. More information go to Gviz (the option "stacking")

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 <- 38290160
end <- 38303219

if(interactive()){
  rmtrack <-repeatMasker_UCSC(gen,chr,start,end,showId=TRUE)
  plotTracks(rmtrack, from = start, to = end)
} else {
  data(repeatMaskerTrack)
  plotTracks(rmtrack, from = start, to = end)
}