Retrieve data files from the Github repository — retrieve_data

This script downloads relevant data files from the CALANGO project repository. It will extract the data into a folder containing directories related to dictionary files, Gene Ontology annotation files, tree files, etc. Note: you may need to edit the file paths in the example scripts contained under the `parameters` subfolder of `target.dir`, or pass an appropriate base path using parameter `basedir` in [run_CALANGO()].

retrieve_data_files(
  target.dir,
  method = "auto",
  unzip = getOption("unzip"),
  ...
)

Arguments

target.dir: path to the folder where the files will be saved ( accepts relative and absolute paths)
method: Method to be used for downloading files. Current download methods are "internal", "wininet" (Windows only) "libcurl", "wget" and "curl", and there is a value "auto": see _Details_ and _Note_ in the documentation of utils::download.file().
unzip: The unzip method to be used. See the documentation of utils::unzip() for details.
...: additional attributes (currently ignored)

Value

No return value, called for side effects (see Description).

Details

If the `target.dir` provided does not exist it is created (recursively) by the function.

Examples

if (FALSE) { # \dontrun{
  CALANGO::retrieve_data_files(target.dir = "./data")
} # }