ensembldb: EnsDb – R documentation

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EnsDb

Connect to an EnsDb object

Description

The EnsDb constructor function connects to the database specified with argument x and returns a corresponding EnsDb object.

Usage

EnsDb(x)

Arguments

`x`	Either a character specifying the SQLite database file, or a `DBIConnection` to e.g. a MariaDB/MySQL database.

Details

By providing the connection to a MariaDB/MySQL database, it is possible to use MariaDB/MySQL as the database backend and queries will be performed on that database. Note however that this requires the package RMariaDB to be installed. In addition, the user needs to have access to a MySQL server providing already an EnsDb database, or must have write privileges on a MySQL server, in which case the useMySQL method can be used to insert the annotations from an EnsDB package into a MySQL database.

Value

A EnsDb object.

Author(s)

Johannes Rainer

Examples

## "Standard" way to create an EnsDb object:
library(EnsDb.Hsapiens.v86)
EnsDb.Hsapiens.v86

## Alternatively, provide the full file name of a SQLite database file
dbfile <- system.file("extdata/EnsDb.Hsapiens.v86.sqlite", package = "EnsDb.Hsapiens.v86")
edb <- EnsDb(dbfile)
edb

## Third way: connect to a MySQL database
## Not run: 
library(RMariaDB)
dbcon <- dbConnect(MySQL(), user = my_user, pass = my_pass,
    host = my_host, dbname = "ensdb_hsapiens_v86")
edb <- EnsDb(dbcon)

## 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