setCustomGenome,igvR-method {igvR} | R 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)
       }

[Package igvR version 1.12.0 Index]