makeTxDbFromEnsembl: Make a TxDb object from an Ensembl database

Description Usage Arguments Value Note Author(s) See Also Examples

View source: R/makeTxDbFromEnsembl.R

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

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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

Examples

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

## End(Not run)

Bioconductor/GenomicFeatures documentation built on May 25, 2021, 5:47 a.m.