getGenomicRegion: Obtain the chromosome and coordiates of the currently...
In paul-shannon/igvR: igvR: integrative genomics viewer

getGenomicRegion,igvR-method

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")
   }

paul-shannon/igvR documentation built on Nov. 11, 2023, 8:26 p.m.