igvR 1.25.0
With the popularity and wide availability of Hi-C data - a high throughput chromatin confirmation capture technology - an appropriate display format was needed. The igv.js team created the Interact track, supporint the bedpe data file format.
We demonstrate this track with a few lines extracted from the Encode project’s ENCFF110BUX experiment, from Michael Snyder’s lab, showing the boundaries and extent of two topologically-associated domains (TADS), typically small genomic regions which are somewhat isolated from neighboring regions, which is believed to play a role in restricting enhancer/promoter interactions.
An equally important, and perhaps more common use of paired-end interaction data is to represent Hi-C maps of enhancer-promoter interactions. These data also rely upon the bedpe file format.
igv.js provides several visualization parameters not yet supported in igvR.
To define a TAD, two genomic locations are required, as shown here and in the code below:
chrom1 start1 end1 chrom2 start2 end2
2 105780000 105790000 2 105890000 105900000
2 105575000 105600000 2 106075000 106100000
These few lines provide a complete, if minimal introduction to the BedpeInteractionsTrack.
library(igvR)
igv <- igvR()
setBrowserWindowTitle(igv, "Paired-end demo")
setGenome(igv, "hg38")
tbl.bedpe <- data.frame(chrom1=c("2","2"),
start1=c(105780000, 105575000),
end1=c(105790000, 105600000),
chrom2=c("2","2"),
start2=c(105890000, 106075000),
end2=c(105900000, 106100000),
stringsAsFactors=FALSE)
# construct a "region of interest" (roi) string from tbl.bedpe
# this is where our two features are found.
shoulder <- 300000
roi <- sprintf("%s:%d-%d", tbl.bedpe$chrom1[1],
min(tbl.bedpe$start1) - shoulder,
max(tbl.bedpe$end2) + shoulder)
showGenomicRegion(igv, roi)
track <- BedpeInteractionsTrack("ENCFF110BUX", tbl.bedpe)
displayTrack(igv, track)
sessionInfo()
#> R version 4.4.0 RC (2024-04-16 r86468)
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#> attached base packages:
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