parseAndValidateGenomeSpec: parseAndValidateGenomeSpec

In paul-shannon/igvShiny: igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data)

parseAndValidateGenomeSpec

Description

a helper function for internal use by the igvShiny constructor, but possible also of use to those building an igvShiny app, to test their genome specification for validity

Usage

parseAndValidateGenomeSpec(
  genomeName,
  initialLocus = "all",
  stockGenome = TRUE,
  dataMode = NA,
  fasta = NA,
  fastaIndex = NA,
  genomeAnnotation = NA
)

Arguments

genomeName	character usually one short code of a supported ("stock") genome (e.g., "hg38") or for a user-supplied custom genome, the name you wish to use
initialLocus	character default "all", otherwise "chrN:start-end" or a recognized gene symbol
stockGenome	logical default TRUE
dataMode	character either "stock", "localFile" or "http"
fasta	character when supplying a custom (non-stock) genome, either a file path or a URL
fastaIndex	character when supplying a custom (non-stock) genome, either a file path or a URL, essential for all but the very small custom genomes.
genomeAnnotation	character when supplying a custom (non-stock) genome, a file path or URL pointing to a genome annotation file in a gff3 format

Value

an options list directly usable by igvApp.js, and thus igv.js

See Also

[get_css_genomes()] for stock genomes we support.

Examples

genomeSpec <-
  parseAndValidateGenomeSpec("hg38", "APOE")  # the simplest case
base.url <-
  "https://gladki.pl/igvr/testFiles/sarsGenome"
fasta.file <-
  sprintf("%s/%s", base.url, "Sars_cov_2.ASM985889v3.dna.toplevel.fa")
fastaIndex.file <-
  sprintf("%s/%s",
          base.url,
          "Sars_cov_2.ASM985889v3.dna.toplevel.fa.fai")
annotation.file <-
  sprintf("%s/%s", base.url, "Sars_cov_2.ASM985889v3.101.gff3")
custom.genome.title <- "SARS-CoV-2"
genomeOptions <-
  parseAndValidateGenomeSpec(
    genomeName = custom.genome.title,
    initialLocus = "all",
    stockGenome = FALSE,
    dataMode = "http",
    fasta = fasta.file,
    fastaIndex = fastaIndex.file,
    genomeAnnotation = annotation.file
  )

paul-shannon/igvShiny documentation built on Aug. 31, 2024, 9:32 a.m.