connectDatabase: Create connection with the MySQL compendium database

In compendiumdb: Tools for Retrieval and Storage of Functional Genomics Data

Description

Allows the user to create a connection with the compendium database in the MySQL server

Usage

connectDatabase(user, password, host = "localhost", dbname = "compendium", port = 3306)

Arguments

user	character string defining the MySQL user name to login to the database
password	character string defining the password required to connect to the MySQL database
host	character string defining the host name. The default value is "localhost". One can also connect to a remote server by defining a valid value for the host name, e.g., "machinename.\domain.\org".
dbname	character string defining the name of the compendium database to which one wants to establish a connection. The default value is "compendium".
port	port number used to connect to the MySQL server. The default port number is 3306.

Details

The compendium database has to be created first, see the package vignette for how to do this from the MySQL prompt.

Value

A list with components

connect	a component of class MySQLConnection containing the connection to the MySQL database
user	character string containing the user name
password	character string containing the password
host	character string containing the host name
port	port number used to connect to the MySQL server
dbname	character string containing the database name

Note

Do not check the returned value of this function, since this might abort the current R session. summary(conn) can be used to check the returned list.

Author(s)

Umesh K. Nandal

Examples

 ## Not run: 
  # Connect to a database with name "compendium"
  conn <- connectDatabase(user="usrname",password="passwd",host="localhost",dbname="compendium")
 
## End(Not run)

compendiumdb documentation built on May 2, 2019, 4:06 p.m.