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.

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=DEFAULT_CIRC_SEQS,
                        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.

- `DEFAULT_CIRC_SEQS`.

- 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)

[Package GenomicFeatures version 1.38.2 Index]