Downloading Ensembl GTF file, creating an SQlite file and accessing the database as an EnsDb object in R

ensembl_sqlite.R

library(ensembldb)

# 1. retrieve the GTF file for Homo sapiens, Ensembl release 114
kEnsemblRelease <- 114
kUrl <- paste0("https://ftp.ensembl.org/pub/release-", kEnsemblRelease, 
               "/gtf/homo_sapiens/",
               "Homo_sapiens.GRCh38.", kEnsemblRelease, ".gtf.gz")
gff_file <- file.path(tempdir(), basename(kUrl))
download.file(kUrl, gff_file)

# 2. Parse the GTF file and create a SQLite database
sqlite_file <- tempfile(fileext = ".sqlite")
dbFile <- ensDbFromGtf(gff_file, outfile = sqlite_file, path = tempdir(),
                       organism = "Homo_sapiens", genomeVersion = "GRCh38",
                       version = )
                       
# 3. Access the SQLite database as an EnsDb object in R
edb <- EnsDb(dbFile)