setCustomGenome: Specify the reference genome you wish to use, via full...

setCustomGenome,igvR-methodR Documentation

Specify the reference genome you wish to use, via full specification of all urls

Description

Specify the reference genome you wish to use, via full specification of all urls

Usage

## S4 method for signature 'igvR'
setCustomGenome(
  obj,
  id,
  genomeName,
  fastaURL,
  fastaIndexURL,
  chromosomeAliasURL = NA,
  cytobandURL = NA,
  geneAnnotationName = NA,
  geneAnnotationURL = NA,
  geneAnnotationTrackHeight = 200,
  geneAnnotationTrackColor = "darkblue",
  initialLocus = "all",
  visibilityWindow = 1e+06
)

Arguments

obj

An object of class igvR

id

character string, a short name, displayed in the browser, e.g., "hg38", "tair10".

genomeName

character string, possibly longer, more descirptive then the id, e.g., "Human (GRCh38/hg38)"

fastaURL

character string, e.g."https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa"

fastaIndexURL

character string, e.g. "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai"

chromosomeAliasURL

character string, default NA, a tab-delimited file supporting multiple equivalent chromosome names. see details

cytobandURL

character string, default NA, a cytoband ideogram file in UCSC format, e.g. "https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/cytoBandIdeo.txt"

geneAnnotationName

character string, e.g. "Refseq Genes", default NA

geneAnnotationURL

character string, e.g. "https://s3.amazonaws.com/igv.org.genomes/hg38/refGene.txt.gz", default NA

geneAnnotationTrackHeight

numeric, pixels, e.g. 500. default 200

geneAnnotationTrackColor

character string, any legal CSS color, default "darkblue"

initialLocus

character string, e.g. "chr5:88,621,308-89,001,037" or "MEF2C"

visibilityWindow

numeric, number of bases over which to display features, default 1000000

Value

An empty string, an error message if any of the urls could not be reached

Examples

if(interactive()){
   igv <- igvR()
   setCustomGenome(igv,
                   id="hg38",
                   genomeName="Human (GRCh38/hg38)",
                   fastaURL="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",
                   fastaIndexURL="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai",
                   chromosomeAliasURL=NA,
                   cytobandURL="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/cytoBandIdeo.txt",
                   geneAnnotationName="Refseq Genes",
                   geneAnnotationURL="https://s3.amazonaws.com/igv.org.genomes/hg38/refGene.txt.gz",
                   geneAnnotationTrackHeight=300,
                   geneAnnotationTrackColor="darkgreen",
                   initialLocus="chr5:88,621,308-89,001,037",
                   visibilityWindow=5000000)
   }


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