segmentalDups_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 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,title="Segmental Dups UCSC")

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

Value

An UcscTrack object of Gviz

Author(s)

Tiphaine Martin

Tom Hardiman

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

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