Connect to an EnsDb object

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

EnsDb(x)

Arguments

x

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

Value

A EnsDb object.

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.

Author

Johannes Rainer

Examples

## "Standard" way to create an EnsDb object:
library(EnsDb.Hsapiens.v86)
EnsDb.Hsapiens.v86
#> EnsDb for Ensembl:
#> |Backend: SQLite
#> |Db type: EnsDb
#> |Type of Gene ID: Ensembl Gene ID
#> |Supporting package: ensembldb
#> |Db created by: ensembldb package from Bioconductor
#> |script_version: 0.3.0
#> |Creation time: Thu May 18 16:32:27 2017
#> |ensembl_version: 86
#> |ensembl_host: localhost
#> |Organism: homo_sapiens
#> |taxonomy_id: 9606
#> |genome_build: GRCh38
#> |DBSCHEMAVERSION: 2.0
#> | No. of genes: 63970.
#> | No. of transcripts: 216741.
#> |Protein data available.

## 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
#> EnsDb for Ensembl:
#> |Backend: SQLite
#> |Db type: EnsDb
#> |Type of Gene ID: Ensembl Gene ID
#> |Supporting package: ensembldb
#> |Db created by: ensembldb package from Bioconductor
#> |script_version: 0.3.0
#> |Creation time: Thu May 18 16:32:27 2017
#> |ensembl_version: 86
#> |ensembl_host: localhost
#> |Organism: homo_sapiens
#> |taxonomy_id: 9606
#> |genome_build: GRCh38
#> |DBSCHEMAVERSION: 2.0
#> | No. of genes: 63970.
#> | No. of transcripts: 216741.
#> |Protein data available.

## Third way: connect to a MySQL database
if (FALSE) {
library(RMariaDB)
dbcon <- dbConnect(MySQL(), user = my_user, pass = my_pass,
    host = my_host, dbname = "ensdb_hsapiens_v86")
edb <- EnsDb(dbcon)
}