makeTxDbFromEnsembl {GenomicFeatures}R Documentation

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.

Usage

makeTxDbFromEnsembl(organism="Homo sapiens",
                    release=NA,
                    circ_seqs=DEFAULT_CIRC_SEQS,
                    server="ensembldb.ensembl.org")

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!

Value

A TxDb object.

Note

makeTxDbFromEnsembl tends to be faster and more reliable than makeTxDbFromBiomart.

Author(s)

H. Pagès

See Also

Examples

txdb <- makeTxDbFromEnsembl("Saccharomyces cerevisiae",
                            server="useastdb.ensembl.org")
txdb

[Package GenomicFeatures version 1.30.3 Index]