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

Description Usage Arguments Value Author(s) References Examples

View source: R/BiofeatureGraphics.R

Description

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

Usage

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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

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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)
}

coMET documentation built on Nov. 1, 2018, 2:17 a.m.