Download Gesel database files — downloadDatabaseFile • gesel

Default function to download Gesel database files.

downloadDatabaseFile(
  name,
  url = databaseUrl(),
  cache = cacheDirectory(),
  overwrite = FALSE
)

databaseUrl(url = NULL)

Arguments

name: String containing the name of a Gesel database file. This usually has the species identifier as a prefix, e.g., "9606_set2gene.tsv.gz".
url: String containing the base URL to the Gesel database files.
cache: String specifying the path to a cache directory.
overwrite: Boolean indicating whether any cached file should be overwritten.

Value

downloadDatabaseFile returns a string containing a path to the downloaded file.

For databaseUrl, if url=NULL, the function returns a string containing the URL to the Gesel database. If url is provided, it instead stores url as the URL to the database, and the previous value of url is invisibly returned.

Details

The database URL defaults to the GitHub releases at https://github.com/LTLA/gesel-feedstock. This can be altered by setting the GESEL_DATABASE_URL environment variable prior to the first call to this function.

Author

Aaron Lun

Examples

# Download file.
downloadDatabaseFile("9606_collections.tsv.gz")
#> [1] "~/.cache/gesel/https%3A%2F%2Fgithub.com%2FLTLA%2Fgesel-feedstock%2Freleases%2Fdownload%2Findices-v0.2.1%2F9606_collections.tsv.gz"

# Altering the default database URL.
databaseUrl()
#> [1] "https://github.com/LTLA/gesel-feedstock/releases/download/indices-v0.2.1"
old <- databaseUrl("https://foo")
databaseUrl()
#> [1] "https://foo"
databaseUrl(old)