In PriceLab/igvR: igvR: integrative genomics viewer

options(width=120)
knitr::opts_chunk$set(
   collapse = TRUE,
   eval=interactive(),
   echo=TRUE,
   comment = "#>"
)

Overview

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.

Example

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

Code

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)

Display

knitr::include_graphics("pairedEnd.png")

Session Info

sessionInfo()

PriceLab/igvR documentation built on Sept. 6, 2022, 5:45 a.m.