makeTxDbFromEnsembl: Make a TxDb object from an Ensembl database

In jmacdon/GenomicFeatures: Conveniently import and query gene models

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

See Also

• makeTxDbFromUCSC and makeTxDbFromBiomart for making a TxDb object from other online resources.

• makeTxDbFromGRanges and makeTxDbFromGFF for making a TxDb object from a GRanges object, or from a GFF or GTF file.

• The TxDb class.

• makeTxDb for the low-level function used by the makeTxDbFrom* functions to make the TxDb object returned to the user.

Examples

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

## End(Not run)

jmacdon/GenomicFeatures documentation built on Jan. 2, 2022, 7:40 a.m.