repeatMasker_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 repeatMasker_UCSC using the Gviz bioconductor package

Usage

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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

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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)
}

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