getGenomicRegion,igvR-method {igvR} | R Documentation

## Obtain the chromosome and coordiates of the currently displayed genomic region.

### Description

Some caution is needed with this function when called right after a lengthy browser operation - of which the main example is display a GenomicAlignmentTrack. igv.js does not at present allow us to delay the return from javascript pending completion of the track rendering. This does not pose much of a problem when you manipulate igv in the browser from R in normal interactive mode: simply wait for your last command to complete. But if you are running in programmatic mode, as we do when testing igvR, then caution is advised. See the test_displayAlignment function in unitTests/test_igvR.R.

### Usage

    ## S4 method for signature 'igvR'
    getGenomicRegion(obj)

### Arguments

`obj` | An object of class igvR

### Value

A list with four fields: chrom (character), start(numeric), end(numeric), string(character)

### Examples

    if(interactive()){
       igv <- igvR()
       setGenome(igv, "hg38")
       showGenomicRegion(igv, "MEF2C")
       getGenomicRegion(igv)
         # list(chrom="chr5", start=88717241, end=88884466, string="chr5:88,717,241-88,884,466")
       }

[Package igvR version 1.6.1 Index]