R in a Nutshell

Use a Database to Query Large Data Sets

If you need to query large tables of data, you should consider storing the values in a database. You don’t need to use an external database; the RSQLite package provides an interface to the SQLite library that allows you to store data in files and query the files using SQL. (This is the strategy that is used by Bioconductor to store annotation databases.) See DBI for more information on how to use this package.