HistoneAll_UCSC: Create multiple tracks of histone modifications from the UCSC...

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

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

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

HistoneOne_UCSC,

Examples

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,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(histonalltrack)
  plotTracks(histonalltrack, from = start, to =end,
                                   fontfamily="sans",fontfamily.title="sans")
}

TiphaineCMartin/coMET documentation built on April 27, 2022, 6:45 a.m.