ensembldb: EnsDb-class – R documentation

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EnsDb-class

Basic usage of an Ensembl based annotation database

Description

The EnsDb class provides access to an Ensembl-based annotation package. This help page describes functions to get some basic informations from such an object.

Usage

## S4 method for signature 'EnsDb'
dbconn(x)

## S4 method for signature 'EnsDb'
ensemblVersion(x)

## S4 method for signature 'EnsDb'
listColumns(x, table, skip.keys=TRUE, ...)

## S4 method for signature 'EnsDb'
listGenebiotypes(x, ...)

## S4 method for signature 'EnsDb'
listTxbiotypes(x, ...)

## S4 method for signature 'EnsDb'
listTables(x, ...)

## S4 method for signature 'EnsDb'
metadata(x, ...)

## S4 method for signature 'EnsDb'
organism(object)

## S4 method for signature 'EnsDb'
returnFilterColumns(x)

## S4 method for signature 'EnsDb'
returnFilterColumns(x)

## S4 replacement method for signature 'EnsDb'
returnFilterColumns(x) <- value

## S4 method for signature 'EnsDb'
seqinfo(x)

## S4 method for signature 'EnsDb'
seqlevels(x)

## S4 method for signature 'EnsDb'
updateEnsDb(x, ...)

Arguments

(in alphabetic order)

`...`	Additional arguments. Not used.
`object`	For `organism`: an `EnsDb` instance.
`skip.keys`	for `listColumns`: whether primary and foreign keys (not being e.g. `"gene_id"` or alike) should be returned or not. By default these will not be returned.
`table`	For `listColumns`: optionally specify the table name(s) for which the columns should be returned.
`value`	For `returnFilterColumns`: a logical of length one specifying whether columns that are used for eventual filters should also be returned.
`x`	An `EnsDb` instance.

Value

For connection: The SQL connection to the RSQLite database.
For EnsDb: An EnsDb instance.
For lengthOf: A named integer vector with the length of the genes or transcripts.
For listColumns: A character vector with the column names.
For listGenebiotypes: A character vector with the biotypes of the genes in the database.
For listTxbiotypes: A character vector with the biotypes of the transcripts in the database.
For listTables: A list with the names corresponding to the database table names and the elements being the attribute (column) names of the table.
For metadata: A data.frame.
For organism: A character string.
For returnFilterColumns: A logical of length 1.
For seqinfo: A Seqinfo class.
For updateEnsDb: A EnsDb object.

Objects from the Class

A connection to the respective annotation database is created upon loading of an annotation package created with the makeEnsembldbPackage function. In addition, the EnsDb constructor specifying the SQLite database file can be called to generate an instance of the object (see makeEnsemblSQLiteFromTables for an example).

Slots

ensdb: Object of class "DBIConnection": the connection to the database.
tables: Named list of database table columns with the names being the database table names. The tables are ordered by their degree, i.e. the number of other tables they can be joined with.
.properties: Internal list storing user-defined properties. Should not be directly accessed.

Methods and Functions

dbconn: Returns the connection to the internal SQL database.
ensemblVersion: Returns the Ensembl version on which the package was built.
listColumns: Lists all columns of all tables in the database, or, if table is specified, of the respective table.
listGenebiotypes: Lists all gene biotypes defined in the database.
listTxbiotypes: Lists all transcript biotypes defined in the database.
listTables: Returns a named list of database table columns (names of the list being the database table names).
metadata: Returns a data.frame with the metadata information from the database, i.e. informations about the Ensembl version or Genome build the database was build upon.
organism: Returns the organism name (e.g. "homo_sapiens").
returnFilterColumns, returnFilterColumns<-: Get or set the option which results in columns that are used for eventually specified filters to be added as result columns. The default value is TRUE (i.e. filter columns are returned).
seqinfo: Returns the sequence/chromosome information from the database.
seqlevels: Returns the chromosome/sequence names that are available in the database.
show: Displays some informations from the database.
updateEnsDb: Updates the EnsDb object to the most recent implementation.

Note

While a column named "tx_name" is listed by the listTables and listColumns method, no such column is present in the database. Transcript names returned by the methods are actually the transcript IDs. This virtual column was only introduced to be compliant with TxDb objects (which provide transcript names).

Author(s)

Johannes Rainer

Examples

library(EnsDb.Hsapiens.v86)

## Display some information:
EnsDb.Hsapiens.v86

## Show the tables along with its columns
listTables(EnsDb.Hsapiens.v86)

## For what species is this database?
organism(EnsDb.Hsapiens.v86)

## What Ensembl version if the database based on?
ensemblVersion(EnsDb.Hsapiens.v86)

## Get some more information from the database
metadata(EnsDb.Hsapiens.v86)

## Get all the sequence names.
seqlevels(EnsDb.Hsapiens.v86)

## List all available gene biotypes from the database:
listGenebiotypes(EnsDb.Hsapiens.v86)

## List all available transcript biotypes:
listTxbiotypes(EnsDb.Hsapiens.v86)

## Update the EnsDb; this is in most instances not necessary at all.
updateEnsDb(EnsDb.Hsapiens.v86)

######    returnFilterColumns
returnFilterColumns(EnsDb.Hsapiens.v86)

## Get protein coding genes on chromosome X, specifying to return
## only columns gene_name as additional column.
genes(EnsDb.Hsapiens.v86, filter=list(SeqNameFilter("X"),
                                      GeneBiotypeFilter("protein_coding")),
      columns=c("gene_name"))
## By default we get also the gene_biotype column as the data was filtered
## on this column.

## This can be changed using the returnFilterColumns option
returnFilterColumns(EnsDb.Hsapiens.v86) <- FALSE
genes(EnsDb.Hsapiens.v86, filter=list(SeqNameFilter("X"),
                                      GeneBiotypeFilter("protein_coding")),
      columns=c("gene_name"))

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