This function calls download.file to download the
pre-build database file of cRegulome. Additionally, the function checks
the validity of the pre-defined URL and whether the database file exists
in the current working directory to avoid redownloading it. Typically,
users would run this function once at the first time the use the package
or to update the database to the latest version.
Arguments
- test
A
logical, defaultFALSE. WhenTRUEdownloads a database file with the same structure with a subset of the data for speed.- destfile
A character vector for the desired path for the database file. By default, when not specified, is constructed by using
tempdiras a directory and the stringcRegulome.db.gz- ...
Optional arguments passed to
download.file
Value
Downloads a compressed sqlite file to the current working
directory. The file is named cRegulome.db.gz by default and it's
not advised to change the name to avoid breaking the other functions
that calls the database.
Examples
if (FALSE) {
# download a test set of the database
get_db(test = TRUE)
# download the full database file
get_db(test = FALSE)
}
# load the test db file from shipped with the pacakge
db_file <- system.file("extdata", "cRegulome.db", package = "cRegulome")
file.info(db_file)
#> size isdir mode
#> /usr/local/lib/R/site-library/cRegulome/extdata/cRegulome.db 1204224 FALSE 644
#> mtime
#> /usr/local/lib/R/site-library/cRegulome/extdata/cRegulome.db 2024-03-30 06:31:52
#> ctime
#> /usr/local/lib/R/site-library/cRegulome/extdata/cRegulome.db 2024-03-30 06:31:56
#> atime
#> /usr/local/lib/R/site-library/cRegulome/extdata/cRegulome.db 2024-03-30 06:32:01
#> uid gid uname
#> /usr/local/lib/R/site-library/cRegulome/extdata/cRegulome.db 0 0 root
#> grname
#> /usr/local/lib/R/site-library/cRegulome/extdata/cRegulome.db root