ensembldb: makeEnsemblDbPackage – R documentation

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makeEnsemblDbPackage

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

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)

ensembldb

Utilities to create and use Ensembl-based annotation databases

v2.14.1

LGPL

Authors

Johannes Rainer <johannes.rainer@eurac.edu> with contributions from Tim Triche, Sebastian Gibb, Laurent Gatto and Christian Weichenberger.

Initial release