HistoneOne_UCSC: Create one track of one histone modification profile from the...

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

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

Author(s)

Tiphaine Martin

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

See Also

HistoneAll_UCSC

Examples

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)
}

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