BedpeInteractionsTrack-class {igvR} | R Documentation

## Constructor for BedpeInteractionsTrack

### Description

`BedpeInteractionsTrack` creates an `IGV` track for two-location annotations

### Usage

    BedpeInteractionsTrack(
      trackName,
      table,
      color = "darkBlue",
      trackHeight = 50,
      displayMode = "EXPANDED",
      visibilityWindow = 1e+05
    )

### Arguments

`trackName` | A character string, used as track label by igv, we recommend unique names per track.
`table` | data.frame of 6 or more columns
`color` | A css color name (e.g., "red" or "#FF0000"
`trackHeight` | track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files)
`displayMode` | "COLLAPSED", "SQUISHED" or "EXPANDED". Spelling and case must be precise.
`visibilityWindow` | Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types.

### Value

A BedpeInteractionsTrack object

### Examples

        #----------------------------
        #  first, from a local file
        #----------------------------

      file <- system.file(package="igvR", "extdata", "sixColumn-demo1.bedpe")
      tbl.bedpe <- read.table(file, sep="\t", as.is=TRUE, header=TRUE)
      dim(tbl.bedpe)  #  32 6
      track <- BedpeInteractionsTrack("bedpe-6", tbl.bedpe)

        #------------------------------------------
        #  show the relevant portion of the genome
        #------------------------------------------

      shoulder <- 10000
      roi <- with(tbl.bedpe, sprintf("%s:%d-%d", chrom1[1], min(start1)-shoulder, max(end2) + shoulder))
      # showGenomicRegion(igv, roi)

      # displayTrack(igv, track)

[Package igvR version 1.12.0 Index]