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

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

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/igvR documentation built on Nov. 17, 2024, 9:36 p.m.