string.raw.to.sqlite: Convert STRING Links Raw Flat File in to SQLite Tables
In dnusinow/snipeR: Software for Network Inference of Proteomics Experiments

Description Usage Arguments Details Value Author(s) See Also Examples

snipeR utilizes STRING in the form of a local SQLite table in order to speed program startup. This function takes the path to the raw file downloaded from the STRING website and outputs a SQLite database for use by snipeR.

1	string.raw.to.sqlite(dbpath = "snipe_maps", force.regen = TRUE)

`dbpath`	The path to the directory where the data files have been downloaded. The SQLite database is also created here. Defaults to "snipe_maps"
`force.regen`	Boolean that determines if, given that the SQLite database already exists, it should be deleted and a new one generated. This provides a safety check against destroying an already existing database and having to wait for a potentially lengthy processing operation to generate the new one. Defaults to `FALSE`.

snipeR requires the STRING database to be accesible. Because this database is distributed as a flat list of links for all species, this can be a very large file to parse each time the snipe function is called. To speed up the process, snipeR expects this file to be processed in to a local relational SQLite database where each table of links is for a single given species. This function takes a path to either the string links file itself or the directory where it is stored and will output a SQLite database in the same directory. This means that the dbpath directory needs to be writable for the user.

Returns TRUE if everything succeeded.

David Nusinow dnusinow@partners.org

snipe, download.missing.maps, string.aliases.to.sqlite.