Description Usage Arguments Value Author(s) References See Also Examples
View source: R/BiofeatureGraphics.R
Create multiple tracks of histone modifications from the UCSC genome browser (ENCODE/Broad) using the Gviz bioconductor package
1 2 |
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 |
A list of AnnotationTrack object of Gviz
Tiphaine Martin
http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=wgEncodeHistoneSuper
http://bioconductor.org/packages/release/bioc/html/Gviz.html
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | 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)
}
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