parseAndValidateGenomeSpec: parseAndValidateGenomeSpec
In PriceLab/igvR: igvR: integrative genomics viewer

parseAndValidateGenomeSpec

R Documentation

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

Examples

genomeSpec <- parseAndValidateGenomeSpec("hg38", "APOE")  # the simplest case
base.url <- "https://igv-data.systemsbiology.net/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)

PriceLab/igvR documentation built on Sept. 6, 2022, 5:45 a.m.