coMET (version 1.4.4)

DNAse_UCSC: Creation of an UCSC's DNase clusters track

Description

Creation of DNase cluster track from a connection to UCSC genome browser in using the GViz bioconductor package

Usage

DNAse_UCSC(gen, chr, start, end, mySession, track.name = "DNase Clusters", 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 DNAse_UCSC. "DNase Clusters"(default)

table.name

the name of the table from the track

Value

An AnnotationTrack object of Gviz

References

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

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

Examples

library("Gviz")
library("rtracklayer")

gen <- "hg19"
chr <- "chr7"
start <- 38290160
end <- 38303219
if(interactive()){
  BROWSER.SESSION="UCSC"
  mySession <- browserSession(BROWSER.SESSION)
  genome(mySession) <- gen
  track.name="Broad ChromHMM"
  tablestrack<-tableNames(ucscTableQuery(mySession, track=track.name))
  table.name<-tablestrack[1]
  dnasetrack<-DNAse_UCSC(gen,chr,start,end,mySession)
  plotTracks(dnasetrack, from = start, to =end)
}else {
    data(dnasetrack)
   plotTracks(dnasetrack, from = start, to =end)
}