listEnsDbs: List EnsDb databases in a MySQL server

In YTLogos/ensembldb: Utilities to create and use Ensembl-based annotation databases

Description

The listEnsDbs function lists EnsDb databases in a MySQL server.

Usage

listEnsDbs(dbcon, host, port, user, pass)

Arguments

dbcon	A DBIConnection object providing access to a MySQL database. Either dbcon or all of the other arguments have to be specified.
host	Character specifying the host on which the MySQL server is running.
port	The port of the MySQL server (usually 3306).
user	The username for the MySQL server.
pass	The password for the MySQL server.

Details

The use of this function requires that the RMySQL package is installed and that the user has either access to a MySQL server with already installed EnsDb databases, or write access to a MySQL server in which case EnsDb databases could be added with the useMySQL method. EnsDb databases follow the same naming conventions than the EnsDb packages, with the exception that the name is all lower case and that "." is replaced by "_".

Value

A data.frame listing the database names, organism name and Ensembl version of the EnsDb databases found on the server.

Author(s)

Johannes Rainer

See Also

useMySQL

Examples

## Not run: 
library(RMySQL)
dbcon <- dbConnect(MySQL(), host = "localhost", user = my_user, pass = my_pass)
listEnsDbs(dbcon)

## End(Not run)

YTLogos/ensembldb documentation built on May 3, 2019, 9:03 p.m.