parseAndValidateGenomeSpec

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

[currently.supported.stock.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)