showGenomicRegion: Set the visible region, by explicit chromLoc string, or by...

showGenomicRegion,igvR-methodR Documentation

Set the visible region, by explicit chromLoc string, or by named features in any curently loaded annotation tracks

Description

Set the visible region, by explicit chromLoc string, or by named features in any curently loaded annotation tracks

Usage

## S4 method for signature 'igvR'
showGenomicRegion(obj, region)

Arguments

obj

An object of class igvR

region

A genomic location (rendered "chr5:9,234,343-9,236,000" or as a list: list(chrom="chr9", start=9234343, end=9236000)) or a labeled annotation in a searchable track, often a gene symbol, eg "MEF2C"

Value

""

Examples

if(interactive()){
   igv <- igvR()
   setGenome(igv, "hg38")
   showGenomicRegion(igv, "MEF2C")
   x <- getGenomicRegion(igv)
      #--------------------
      # zoom out 2kb
      #--------------------
   showGenomicRegion(igv, with(x, sprintf("%s:%d-%d", chrom, start-1000, end+1000)))
   }


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