HistoneOne_UCSC: Create one track of one histone modification profile from the UCSC genome browser

Description

Create one track of one histone modification profile from the UCSC genome browser (ENCODE/Broad) using the Gviz bioconductor package

Usage

HistoneOne_UCSC(gen, chr, start, end, mySession, track.name = "Broad Histone", table.name = NULL)

Arguments

gen

the name of the genome. Data is not currently available for GRCh38 (hg38).

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)

mySession

the object session from the function browserSession of rtracklayer

track.name

the name of the track, for example: "Broad Histone"

table.name

the name of the table from the track

Value

An AnnotationTrack object of Gviz

References

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=wgEncodeHistoneSuper

http://bioconductor.org/packages/release/bioc/html/Gviz.html

Examples

Run this code

library("Gviz")
library("rtracklayer")
gen <- "hg19"
chr <- "chr2"
start <- 38290160
end <- 38303219

if(interactive()) {
  BROWSER.SESSION="UCSC"
  mySession <- browserSession(BROWSER.SESSION)
  genome(mySession) <- gen
  histoneonetrack<-HistoneOne_UCSC(gen,chr,start,end,mySession)
  plotTracks(histoneonetrack, from = start, to =end)
} else {
  data(histoneonetrack)
  plotTracks(histoneonetrack, from = start, to =end)
}