CoxpresDbAccessor: Constructor for the CoxpresDbAccessor class - Use this to...
In russHyde/coxpresdbr: Parses and Summarises Data from coxpresdb.jp

Description Usage Arguments Details Value

The db_archive should be a data-frame, a .zip, .tar or a .tar.bz2.

1 2	CoxpresDbAccessor(db_archive, temp_dir = tempdir(), overwrite_in_bunzip2 = FALSE, remove_in_bunzip2 = FALSE)

`db_archive`	Either a data-frame or a file path. If a file-path, it should be a single ``.tar.bz2, ``.tar, or `*`.zip file as downloaded from the _coxpresdb.jp_ website. If a data-frame it should have columns `source_id`, `target_id` and `mutual_rank`.
`temp_dir`	A directory into which a compressed CoxpresDB archive will be decompressed. By default this is the temp_dir for the current R session. Only relevant if the coxpresdb archive is compressed.
`overwrite_in_bunzip2`	Boolean. If the CoxpresDB archive is compressed, and a decompressed copy of the archive is found in the target directory, should the function throw an exception? See `overwrite` in `R.utils::bunzip2`
`remove_in_bunzip2`	Boolean. If a compressed CoxpresDB archive is provided, should the compressed version be deleted after decompression? See `remove` in `R.utils::bunzip2`

If db_archive is a .tar.bz2 then temp_dir should be defined and a random copy of the uncompressed archive will be made. All access to the stored data will be made via the uncompressed copy of the archive, so make a CoxpresDbAccessor _once_ during any given script.

Data-frame access is the fastest approach (but works 'in memory'). Access via an archive is useful if you want to set up a reduced-size coxpresDB file for subsequent 'in-memory' use in your analysis workflow.

A CoxpresDbAccessor object.

russHyde/coxpresdbr documentation built on Dec. 24, 2019, 11:59 a.m.