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

setCustomGenome.Rd

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

Usage

# S4 method for 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)
   }