makeEnsembldbPackage {ensembldb} | R Documentation

## Generating a Ensembl annotation package from Ensembl

### Description

The functions described on this page allow to build `EnsDb` annotation objects/databases from Ensembl annotations. The most complete set of annotations, which include also the NCBI Entrezgene identifiers for each gene, can be retrieved by the functions using the Ensembl Perl API (i.e. functions `fetchTablesFromEnsembl`, `makeEnsemblSQLiteFromTables`). Alternatively the functions `ensDbFromAH`, `ensDbFromGRanges`, `ensDbFromGff` and `ensDbFromGtf` can be used to build `EnsDb` objects using GFF or GTF files from Ensembl, which can be either manually downloaded from the Ensembl ftp server, or directly form within R using `AnnotationHub`. The generated SQLite database can be packaged into an R package using the `makeEnsembldbPackage`.

### Usage

    ensDbFromAH(ah, outfile, path, organism, genomeVersion, version)

    ensDbFromGRanges(x, outfile, path, organism, genomeVersion,
                     version, ...)

    ensDbFromGff(gff, outfile, path, organism, genomeVersion,
                 version, ...)

    ensDbFromGtf(gtf, outfile, path, organism, genomeVersion,
                 version, ...)

    fetchTablesFromEnsembl(version, ensemblapi, user="anonymous",
                           host="ensembldb.ensembl.org", pass="",
                           port=5306, species="human")

    makeEnsemblSQLiteFromTables(path=".", dbname)

    makeEnsembldbPackage(ensdb, version, maintainer, author,
                         destDir=".", license="Artistic-2.0")

### Arguments

(in alphabetical order)

`ah` | For `ensDbFromAH`: an `AnnotationHub` object representing a single resource (i.e. GTF file from Ensembl) from `AnnotationHub`.
`author` | The author of the package.
`dbname` | The name for the database (optional). By default a name based on the species and Ensembl version will be automatically generated (and returned by the function).
`destDir` | Where the package should be saved to.
`ensdb` | The file name of the SQLite database generated by `makeEnsemblSQLiteFromTables`.
`ensemblapi` | The path to the Ensembl perl API installed locally on the system. The Ensembl perl API version has to fit the version.
`genomeVersion` | For `ensDbFromAH`, `ensDbFromGtf` and `ensDbFromGff`: the version of the genome (e.g. `"GRCh37"`). If not provided the function will try to guess it from the file name (assuming file name convention of Ensembl GTF files).
`gff` | The GFF file to import.
`gtf` | The GTF file name.
`host` | The hostname to access the Ensembl database.
`license` | The license of the package.
`maintainer` | The maintainer of the package.
`organism` | For `ensDbFromAH`, `ensDbFromGff` and `ensDbFromGtf`: the organism name (e.g. `"Homo_sapiens"`). If not provided the function will try to guess it from the file name (assuming file name convention of Ensembl GTF files).
`outfile` | The desired file name of the SQLite file. If not provided the name of the GTF file will be used.
`pass` | The password for the Ensembl database.
`path` | The directory in which the tables retrieved by `fetchTablesFromEnsembl` or the SQLite database file generated by `ensDbFromGtf` are stored.
`port` | The port to be used to connect to the Ensembl database.
`species` | The species for which the annotations should be retrieved.
`user` | The username for the Ensembl database.
`version` | For `fetchTablesFromEnsembl`, `ensDbFromGRanges` and `ensDbFromGtf`: the Ensembl version for which the annotation should be retrieved (e.g. 75). The `ensDbFromGtf` function will try to guess the Ensembl version from the GTF file name if not provided. For `makeEnsemblDbPackage`: the version for the package.
`x` | For `ensDbFromGRanges`: the `GRanges` object.
`...` | Currently not used.

### Details

The `fetchTablesFromEnsembl` function internally calls the perl script `get_gene_transcript_exon_tables.pl` to retrieve all required information from the Ensembl database using the Ensembl perl API.

As an alternative way, a EnsDb database file can be generated by the `ensDbFromGtf` or `ensDbFromGff` from a GTF or GFF file downloaded from the Ensembl ftp server or using the `ensDbFromAH` to build a database directly from corresponding resources from the AnnotationHub. The returned database file name can then be used as an input to the `makeEnsembldbPackage` or it can be directly loaded and used by the `EnsDb` constructor.

### Value

`makeEnsemblSQLiteFromTables`, `ensDbFromAH`, `ensDbFromGRanges` and `ensDbFromGtf`: the name of the SQLite file.

### Functions

ensDbFromAH

  Create an `EnsDb` (SQLite) database from a GTF file provided by `AnnotationHub`. The function returns the file name of the generated database file. For usage see the examples below.

ensDbFromGff

  Create an `EnsDb` (SQLite) database from a GFF file from Ensembl. The function returns the file name of the generated database file. For usage see the examples below.

ensDbFromGtf

  Create an `EnsDb` (SQLite) database from a GTF file from Ensembl. The function returns the file name of the generated database file. For usage see the examplesbelow.

ensDbFromGRanges

  Create an `EnsDb` (SQLite) database from a GRanges object (e.g. from `AnnotationHub`). The function returns the file name of the generated database file. For usage see the examples below.

fetchTablesFromEnsembl

  Uses the Ensembl Perl API to fetch all required data from an Ensembl database server and stores them locally to text files (that can be used as input for the `makeEnsembldbSQLiteFromTables` function).

makeEnsemblSQLiteFromTables

  Creates the SQLite `EnsDb` database from the tables generated by the `fetchTablesFromEnsembl`.

makeEnsembldbPackage

  Creates an R package containing the `EnsDb` database from a `EnsDb` SQLite database created by any of the above functions `ensDbFromAH`, `ensDbFromGff`, `ensDbFromGtf` or `makeEnsemblSQLiteFromTables`.

### Note

A local installation of the Ensembl perl API is required for the `fetchTablesFromEnsembl`. See http://www.ensembl.org/info/docs/api/api_installation.html for installation inscructions.

A database generated from a GTF/GFF files lacks some features as they are not available in the GTF files from Ensembl. These are: NCBI Entrezgene IDs.

### Author(s)

Johannes Rainer

### See Also

`EnsDb`, `genes`

### Examples

    ## Not run:

        ## get all human gene/transcript/exon annotations from Ensembl (75)
        ## the resulting tables will be stored by default to the current working
        ## directory; if the correct Ensembl api (version 75) is defined in the
        ## PERL5LIB environment variable, the ensemblapi parameter can also be omitted.
        fetchTablesFromEnsembl(75,
                               ensemblapi="/home/bioinfo/ensembl/75/API/ensembl/modules",
                               species="human")

        ## These tables can then be processed to generate a SQLite database
        ## containing the annotations
        DBFile <- makeEnsemblSQLiteFromTables()

        ## and finally we can generate the package
        makeEnsembldbPackage(ensdb=DBFile, version="0.0.1",
                             maintainer="Johannes Rainer <johannes.rainer@eurac.edu>",
                             author="J Rainer")

        ## Build an annotation database form a GFF file from Ensembl.
        ## ftp://ftp.ensembl.org/pub/release-83/gff3/rattus_norvegicus
        gff <- "Rattus_norvegicus.Rnor_6.0.83.gff3.gz"
        DB <- ensDbFromGff(gff=gff)
        edb <- EnsDb(DB)
        edb

        ## Build an annotation file from a GTF file.
        ## the GTF file can be downloaded from
        ## ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/
        gtffile <- "Homo_sapiens.GRCh37.75.gtf.gz"
        ## generate the SQLite database file
        DB <- ensDbFromGtf(gtf=paste0(ensemblhost, gtffile))

        ## load the DB file directly
        EDB <- EnsDb(DB)

        ## Alternatively, we could fetch a GTF file directly from AnnotationHub
        ## and build the database from that:
        library(AnnotationHub)
        ah <- AnnotationHub()
        ## Query for all GTF files from Ensembl for Ensembl version 81
        query(ah, c("Ensembl", "release-81", "GTF"))
        ## We could get the one from e.g. Bos taurus:
        DB <- ensDbFromAH(ah["AH47941"])
        edb <- EnsDb(DB)
        edb

    ## End(Not run)

    ## Generate a sqlite database for genes encoded on chromosome Y
    chrY <- system.file("chrY", package="ensembldb")
    DBFile <- makeEnsemblSQLiteFromTables(path=chrY ,dbname=tempfile())
    ## load this database:
    edb <- EnsDb(DBFile)

    edb

    ## Generate a sqlite database from a GRanges object specifying
    ## genes encoded on chromosome Y
    load(system.file("YGRanges.RData", package="ensembldb"))

    Y

    DB <- ensDbFromGRanges(Y, path=tempdir(), version=75,
                           organism="Homo_sapiens")
    edb <- EnsDb(DB)

[Package ensembldb version 2.12.1 Index]