GenomicFeatures: makeTxDbFromEnsembl – R documentation

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makeTxDbFromEnsembl

Make a TxDb object from an Ensembl database

Description

The makeTxDbFromEnsembl function creates a TxDb object for a given organism by importing the genomic locations of its transcripts, exons, CDS, and genes from an Ensembl database.

Note that it uses the RMariaDB package internally so make sure that this package is installed.

Usage

makeTxDbFromEnsembl(organism="Homo sapiens",
                    release=NA,
                    circ_seqs=NULL,
                    server="ensembldb.ensembl.org",
                    username="anonymous", password=NULL, port=0L,
                    tx_attrib=NULL)

Arguments

`organism`	The scientific name (i.e. genus and species, or genus and species and subspecies) of the organism for which to import the data. Case is not sensitive. Underscores can be used instead of white spaces e.g. `"homo_sapiens"` is accepted.
`release`	The Ensembl release to query e.g. 89. If set to `NA` (the default), the current release is used.
`circ_seqs`	A character vector to list out which chromosomes should be marked as circular.
`server`	The name of the MySQL server to query. See https://www.ensembl.org/info/data/mysql.html for the list of Ensembl public MySQL servers. Make sure to use the server nearest to you. It can make a big difference!
`username`	Login username for the MySQL server.
`password`	Login password for the MySQL server.
`port`	Port of the MySQL server.
`tx_attrib`	If not `NULL`, only select transcripts with an attribute of the given code, a string, like `"gencode_basic"`.

Value

A TxDb object.

Note

makeTxDbFromEnsembl tends to be faster and more reliable than makeTxDbFromBiomart.

Author(s)

H. Pagès

Examples

## Not run: 
txdb <- makeTxDbFromEnsembl("Saccharomyces cerevisiae",
                            server="useastdb.ensembl.org")
txdb

## End(Not run)

GenomicFeatures

Conveniently import and query gene models

v1.42.3

Artistic-2.0

Authors

M. Carlson, H. Pagès, P. Aboyoun, S. Falcon, M. Morgan, D. Sarkar, M. Lawrence, V. Obenchain

Initial release