DNAse_UCSC: Creation of an UCSC's DNase clusters track

In TiphaineCMartin/coMET_original: coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.

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

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=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)
}

TiphaineCMartin/coMET_original documentation built on May 9, 2019, 4:49 p.m.