igvR 1.18.1
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"
With the output filename blank, the get output button shows you the selected data as text in your web browser:
Return to the previous UCSC Table Browser Screen, fill in a download filename, click get output
tbl <- read.table("~/drop/k562-h3k4me3-gata2.tsv", sep="\t", skip=1, as.is=TRUE, fill=TRUE)
colnames(tbl) <- c("chrom", "start", "end", "score")
Make sure the column classes are as expected:
lapply(tbl, class)
$chrom
[1] "character"
$start
[1] "integer"
$end
[1] "integer"
$score
[1] "numeric"
track <- DataFrameQuantitativeTrack("H3K4Me3 K562", tbl, autoscale=TRUE, color="darkGreen")
displayTrack(igv, track)
sessionInfo()
#> R version 4.2.2 (2022-10-31)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.5 LTS
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#> Matrix products: default
#> BLAS: /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
#> LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_GB LC_COLLATE=C
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
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#> other attached packages:
#> [1] BiocStyle_2.26.0
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#> loaded via a namespace (and not attached):
#> [1] bookdown_0.33 digest_0.6.31 R6_2.5.1 jsonlite_1.8.4 evaluate_0.20
#> [6] highr_0.10 cachem_1.0.7 rlang_1.0.6 cli_3.6.0 jquerylib_0.1.4
#> [11] bslib_0.4.2 rmarkdown_2.20 tools_4.2.2 xfun_0.37 yaml_2.3.7
#> [16] fastmap_1.1.1 compiler_4.2.2 BiocManager_1.30.20 htmltools_0.5.4 knitr_1.42
#> [21] sass_0.4.5