HistoneAll_UCSC: Create multiple tracks of histone modifications from the UCSC genome browser

Description

Create multiple tracks of histone modifications from the UCSC genome browser (ENCODE/Broad) using the Gviz bioconductor package

Usage

HistoneAll_UCSC(gen, chr, start, end, mySession, pattern = NULL, 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

pattern

The cell type

track.name

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

table.name

the name of the table from the track

Value

A list of 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 <- 38313219

if(interactive()){
  BROWSER.SESSION="UCSC"
  mySession <- browserSession(BROWSER.SESSION)
  genome(mySession) <- gen
  pattern1 <- "GM12878"

  histonalltrack<-HistoneAll_UCSC(gen,chr,start,end,mySession, pattern=pattern1,track.name="Broad Histone")
  plotTracks(histonalltrack, from = start, to =end)
} else {
  data(histonalltrack)
  plotTracks(histonalltrack, from = start, to =end)
}