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

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

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, title="RepeatMasker",
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)
title	The name of the annotation track
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

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

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