GenomicFeatures (version 1.24.4)

makeTxDbFromBiomart: Make a TxDb object from annotations available on a BioMart database

Description

The makeTxDbFromBiomart function allows the user to make a TxDb object from transcript annotations available on a BioMart database.

Usage

makeTxDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", transcript_ids=NULL, circ_seqs=DEFAULT_CIRC_SEQS, filter=NULL, id_prefix="ensembl_", host="www.ensembl.org", port=80, taxonomyId=NA, miRBaseBuild=NA)
getChromInfoFromBiomart(biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", id_prefix="ensembl_", host="www.ensembl.org", port=80)

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'.

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=list(source="entrez")

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_".

host

The host URL of the BioMart. Defaults to www.ensembl.org.

port

The port to use in the HTTP communication with the host.

taxonomyId

By default this value is NA and the dataset selected will be used to look up the correct value for this. But you can use this argument to override that and supply your own taxId here (which will be independently checked to make sure its a real taxonomy id). Normally you should never need to use this.

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.

Value

A TxDb object for makeTxDbFromBiomart.A data frame with 1 row per chromosome (or scaffold) and with columns chrom and length for getChromInfoFromBiomart.

Details

makeTxDbFromBiomart is a convenience function that feeds data from a BioMart database to the lower level makeTxDb function. See ?makeTxDbFromUCSC for a similar function that feeds data from the UCSC source.

Here is a list of datasets known to be compatible with makeTxDbFromBiomart (updated on November 12, 2015):

• All the datasets in the main Ensembl database (list them with biomaRt::listDatasets(biomaRt::useMart( biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org"))).

All the datasets in the Ensembl Fungi database (list them with biomaRt::listDatasets(biomaRt::useMart( biomart="fungal_mart", host="fungi.ensembl.org"))).

All the datasets in the Ensembl Metazoa database (list them with biomaRt::listDatasets(biomaRt::useMart( biomart="metazoa_mart", host="metazoa.ensembl.org"))).

All the datasets in the Ensembl Plants database (list them with biomaRt::listDatasets(biomaRt::useMart( biomart="plants_mart", host="plants.ensembl.org"))).

All the datasets in the Ensembl Protists database (list them with biomaRt::listDatasets(biomaRt::useMart( biomart="protist_mart", host="protists.ensembl.org"))).

All the datasets in the Gramene Mart (list them with biomaRt::listDatasets(biomaRt::useMart( biomart="ENSEMBL_MART_PLANT", host="ensembl.gramene.org"))).

Not all these datasets have CDS information.

See Also

• makeTxDbFromUCSC, makeTxDbFromGRanges, and makeTxDbFromGFF, for convenient ways to make a TxDb object from UCSC online resources, or from a GRanges object, or from a GFF or GTF file.

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

• DEFAULT_CIRC_SEQS.

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

• The TxDb class.

• makeTxDb for the low-level function used by the makeTxDbFrom* functions to make the TxDb object returned to the user.

Examples

## ---------------------------------------------------------------------
## A. BASIC USAGE
## ---------------------------------------------------------------------

## We can use listDatasets() from the biomaRt package to list the
## datasets available in the "ENSEMBL_MART_ENSEMBL" BioMart database:
library(biomaRt)
listMarts(host="www.ensembl.org")
datasets <- listDatasets(useMart(biomart="ENSEMBL_MART_ENSEMBL",
                                 host="www.ensembl.org"))
head(datasets)
subset(datasets, grepl("elegans", dataset, ignore.case=TRUE))

## Retrieve the full transcript dataset for Worm:
txdb1 <- makeTxDbFromBiomart(dataset="celegans_gene_ensembl")
txdb1

## Retrieve an incomplete transcript dataset for Human:
transcript_ids <- c(
    "ENST00000013894",
    "ENST00000268655",
    "ENST00000313243",
    "ENST00000435657",
    "ENST00000384428",
    "ENST00000478783"
)
txdb2 <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl",
                             transcript_ids=transcript_ids)
txdb2  # note that these annotations match the GRCh38 genome assembly

## ---------------------------------------------------------------------
## B. USING A HOST OTHER THAN www.ensembl.org
## ---------------------------------------------------------------------

## A typical use case is to access the "ENSEMBL_MART_ENSEMBL" BioMart
## database on a mirror e.g. on uswest.ensembl.org. A gotcha when
## doing this is that the name of the database on the mirror might
## be different! We can check this with listMarts() from the biomaRt
## package:
listMarts(host="useast.ensembl.org")

## Therefore in addition to setting 'host' to "uswest.ensembl.org" we
## might also need to specify the 'biomart' argument:
txdb3 <- makeTxDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL",
                             dataset="hsapiens_gene_ensembl",
                             transcript_ids=transcript_ids,
                             host="useast.ensembl.org")
txdb3

## ---------------------------------------------------------------------
## C. USING FILTERS
## ---------------------------------------------------------------------

## We can use listFilters() from the biomaRt package to get valid filter
## names:
mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL",
                dataset="hsapiens_gene_ensembl",
                host="www.ensembl.org")
head(listFilters(mart))

## Retrieve transcript dataset for Ensembl gene ENSG00000011198:
my_filter <- list(ensembl_gene_id="ENSG00000011198")
txdb4 <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl",
                             filter=my_filter)
txdb4
transcripts(txdb4, columns=c("tx_id", "tx_name", "gene_id"))
transcriptLengths(txdb4)

## ---------------------------------------------------------------------
## D. RETRIEVING CHROMOSOME INFORMATION ONLY
## ---------------------------------------------------------------------

chrominfo <- getChromInfoFromBiomart(dataset="celegans_gene_ensembl")
chrominfo