makeOrganismDbFromBiomart: Make a OrganismDb object from annotations available on a...

In Bioconductor/OrganismDbi: Software to enable the smooth interfacing of different database packages

Make a OrganismDb object from annotations available on a BioMart database

Description

The makeOrganismDbFromBiomart function allows the user to make a OrganismDb object from transcript annotations available on a BioMart database. This object has all the benefits of a TxDb, plus an associated OrgDb and GODb object.

Usage

makeOrganismDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL",
                    dataset="hsapiens_gene_ensembl",
                    transcript_ids=NULL,
                    circ_seqs=NULL,
                    filter="",
                    id_prefix="ensembl_",
                    host="https://www.ensembl.org",
                    port,
                    miRBaseBuild=NA,
                    keytype = "ENSEMBL",
                    orgdb = NA)

Arguments

biomart	which BioMart database to use. Get the list of all available BioMart databases with the listMarts function from the biomaRt package. See the details section below for a list of BioMart databases with compatible transcript annotations.
dataset	which dataset from BioMart. For example: "hsapiens_gene_ensembl", "mmusculus_gene_ensembl", "dmelanogaster_gene_ensembl", "celegans_gene_ensembl", "scerevisiae_gene_ensembl", etc in the ensembl database. See the examples section below for how to discover which datasets are available in a given BioMart database.
transcript_ids	optionally, only retrieve transcript annotation data for the specified set of transcript ids. If this is used, then the meta information displayed for the resulting TxDb object will say 'Full dataset: no'. Otherwise it will say 'Full dataset: yes'. This TxDb object will be embedded in the resulting OrganismDb object.
circ_seqs	a character vector to list out which chromosomes should be marked as circular.
filter	Additional filters to use in the BioMart query. Must be a named list. An example is filter=as.list(c(source="entrez"))
host	The host URL of the BioMart. Defaults to www.ensembl.org.
port	Deprecated: The port to use in the HTTP communication with the host.
id_prefix	Specifies the prefix used in BioMart attributes. For example, some BioMarts may have an attribute specified as "ensembl_transcript_id" whereas others have the same attribute specified as "transcript_id". Defaults to "ensembl_".
miRBaseBuild	specify the string for the appropriate build Information from mirbase.db to use for microRNAs. This can be learned by calling supportedMiRBaseBuildValues. By default, this value will be set to NA, which will inactivate the microRNAs accessor.
keytype	This indicates the kind of key that this database will use as a foreign key between it's TxDb object and it's OrgDb object. So basically whatever the column name is for the foreign key from your OrgDb that your TxDb will need to map it's GENEID on to. By default it is "ENSEMBL" since the GENEID's for most biomaRt based TxDbs will be ensembl gene ids and therefore they will need to map to ENSEMBL gene mappings from the associated OrgDb object.
orgdb	By default, makeOrganismDbFromBiomart will use the taxonomyID from your txdb to lookup an appropriate matching OrgDb object but using this you can supply a different OrgDb object.

Details

makeOrganismDbFromBiomart is a convenience function that feeds data from a BioMart database to the lower level OrganismDb constructor. See ?makeOrganismDbFromUCSC for a similar function that feeds data from the UCSC source.

The listMarts function from the biomaRt package can be used to list all public BioMart databases. Not all databases returned by this function contain datasets that are compatible with (i.e. understood by) makeOrganismDbFromBiomart. Here is a list of datasets known to be compatible (updated on Sep 24, 2014):

• All the datasets in the main Ensembl database: use biomart="ensembl".

• All the datasets in the Ensembl Fungi database: use biomart="fungi_mart_XX" where XX is the release version of the database e.g. "fungi_mart_22".

• All the datasets in the Ensembl Metazoa database: use biomart="metazoa_mart_XX" where XX is the release version of the database e.g. "metazoa_mart_22".

• All the datasets in the Ensembl Plants database: use biomart="plants_mart_XX" where XX is the release version of the database e.g. "plants_mart_22".

• All the datasets in the Ensembl Protists database: use biomart="protists_mart_XX" where XX is the release version of the database e.g. "protists_mart_22".

• All the datasets in the Gramene Mart: use biomart="ENSEMBL_MART_PLANT".

Not all these datasets have CDS information.

Value

A OrganismDb object.

Author(s)

M. Carlson

See Also

• makeOrganismDbFromUCSC for convenient ways to make a OrganismDb object from UCSC online resources.

• The listMarts, useMart, and listDatasets functions in the biomaRt package.

• The supportedMiRBaseBuildValues function for listing all the possible values for the miRBaseBuild argument.

• The OrganismDb class.

Examples

## Discover which datasets are available in the "ensembl" BioMart
## database:
library(biomaRt)
mart <- useEnsembl("ensembl")
datasets <- listDatasets(mart)
head(datasets)

## Retrieving an incomplete transcript dataset for Human from the
## "ensembl" BioMart database:
transcript_ids <- c(
    "ENST00000013894",
    "ENST00000268655",
    "ENST00000313243",
    "ENST00000435657",
    "ENST00000384428",
    "ENST00000478783"
)
odb <- makeOrganismDbFromBiomart(transcript_ids=transcript_ids)
odb  # note that these annotations match the GRCh38 genome assembly

if (interactive()) {
  ## Now what if we want to use another mirror?  We might make use of the
  ## new host argument.  But wait!  If we use biomaRt, we can see that
  ## this host has named the mart differently!
  listMarts(host="https://useast.ensembl.org")

  ## Therefore we must also change the name passed into the "mart"
  ## argument thusly:
  makeOrganismDbFromBiomart(
      biomart="ENSEMBL_MART_ENSEMBL",
      transcript_ids=transcript_ids,
      host="https://useast.ensembl.org"
  )
}

Bioconductor/OrganismDbi documentation built on Nov. 2, 2024, 7:20 a.m.