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

In paul-shannon/IGV: igvR: integrative genomics viewer

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/IGV documentation built on Nov. 5, 2023, 2:09 p.m.