igvR 1.25.0
The UCSC Table Browser is a good source of genomic annotations of many different kinds. It has a clear, easily navigated user interface. It is a good complement to igvR.
The H3K4Me3 post-translational modification is frequently found in active promoters near transcription start sites. Here we obtain H3K4Me3 methylation marks in K562 cells in and around GATA2.
These are the steps involved:
All these steps are shown below.
library(igvR)
igv <- igvR()
setBrowserWindowTitle(igv, "H3K4Me3 GATA2")
setGenome(igv, "hg38")
showGenomicRegion(igv, "GATA2")
zoomOut(igv)
zoomOut(igv)
getGenomicRegion(igv)
$chrom
[1] "chr3"
$start
[1] 128454762
$end
[1] 128517865
$width
[1] 63104
$string
[1] "chr3:128,454,762-128,517,865"