ensembldb: useMySQL-EnsDb-method – R documentation

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useMySQL-EnsDb-method

Use a MariaDB/MySQL backend

Description

Change the SQL backend from SQLite to MySQL. When first called on an EnsDb object, the function tries to create and save all of the data into a MySQL database. All subsequent calls will connect to the already existing MySQL database.

Usage

## S4 method for signature 'EnsDb'
useMySQL(x, host = "localhost", port = 3306, user, pass)

Arguments

`x`	The `EnsDb` object.
`host`	Character vector specifying the host on which the MariaDB/MySQL server runs.
`port`	The port on which the MariaDB/MySQL server can be accessed.
`user`	The user name for the MariaDB/MySQL server.
`pass`	The password for the MariaDB/MySQL server.

Details

This functionality requires that the RMariaDB package is installed and that the user has (write) access to a running MySQL server. If the corresponding database does already exist users without write access can use this functionality.

Value

A EnsDb object providing access to the data stored in the MySQL backend.

Note

At present the function does not evaluate whether the versions between the SQLite and MariaDB/MySQL database differ.

Author(s)

Johannes Rainer

Examples

## Load the EnsDb database (SQLite backend).
library(EnsDb.Hsapiens.v86)
edb <- EnsDb.Hsapiens.v86
## Now change the backend to MySQL; my_user and my_pass should
## be the user name and password to access the MySQL server.
## Not run: 
edb_mysql <- useMySQL(edb, host = "localhost", user = my_user, pass = my_pass)

## End(Not run)

ensembldb

Utilities to create and use Ensembl-based annotation databases

v2.14.1

LGPL

Authors

Johannes Rainer <johannes.rainer@eurac.edu> with contributions from Tim Triche, Sebastian Gibb, Laurent Gatto and Christian Weichenberger.

Initial release