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

In jmacdon/GenomicFeatures: Conveniently import and query gene models

Description

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

Note that makeTxDbFromBiomart is being phased out in favor of makeTxDbFromEnsembl.

Usage

makeTxDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL",
                    dataset="hsapiens_gene_ensembl",
                    transcript_ids=NULL,
                    circ_seqs=NULL,
                    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.

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 (list updated on September 18, 2017):

1. All the datasets in the main Ensembl database. Get the list with:

       mart <- biomaRt::useMart(biomart="ENSEMBL_MART_ENSEMBL",
                                host="www.ensembl.org")
       biomaRt::listDatasets(mart)

2. All the datasets in the Ensembl Fungi database. Get the list with:

       mart <- biomaRt::useMart(biomart="fungi_mart",
                                host="fungi.ensembl.org")
       biomaRt::listDatasets(mart)

3. All the datasets in the Ensembl Metazoa database. Get the list with:

       mart <- biomaRt::useMart(biomart="metazoa_mart",
                                host="metazoa.ensembl.org")
       biomaRt::listDatasets(mart)

4. All the datasets in the Ensembl Plants database. Get the list with:

       mart <- biomaRt::useMart(biomart="plants_mart",
                                host="plants.ensembl.org")
       biomaRt::listDatasets(mart)

5. All the datasets in the Ensembl Protists database. Get the list with:

       mart <- biomaRt::useMart(biomart="protists_mart",
                                host="protists.ensembl.org")
       biomaRt::listDatasets(mart)

6. All the datasets in the Gramene Mart. Get the list with:

       mart <- biomaRt::useMart(biomart="ENSEMBL_MART_PLANT",
                                host="ensembl.gramene.org")
       biomaRt::listDatasets(mart)

Note that BioMart is not currently available for Ensembl Bacteria.

Also please note that not all these datasets have CDS information.

Value

A TxDb object for makeTxDbFromBiomart.

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

Author(s)

M. Carlson and H. Pagès

See Also

• makeTxDbFromUCSC and makeTxDbFromEnsembl 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.

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

• 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")
mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")
datasets <- listDatasets(mart)
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"
)

if (interactive()) {
  txdb2 <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl",
                               transcript_ids=transcript_ids)
  txdb2  # note that these annotations match the GRCh38 genome assembly
}

## ---------------------------------------------------------------------
## B. ACCESSING THE EnsemblGenomes MARTS
## ---------------------------------------------------------------------

library(biomaRt)

## Note that BioMart is not currently available for Ensembl Bacteria.

## ---------------------
## --- Ensembl Fungi ---

mart <- useMart(biomart="fungi_mart", host="fungi.ensembl.org")
datasets <- listDatasets(mart)
datasets$dataset
yeast_txdb <- makeTxDbFromBiomart(biomart="fungi_mart",
                                  dataset="scerevisiae_eg_gene",
                                  host="fungi.ensembl.org")
yeast_txdb

## Note that the dataset for Yeast on Ensembl Fungi is not necessarily
## the same as on the main Ensembl database:
yeast_txdb0 <- makeTxDbFromBiomart(dataset="scerevisiae_gene_ensembl")
all(transcripts(yeast_txdb0) %in% transcripts(yeast_txdb))
all(transcripts(yeast_txdb) %in% transcripts(yeast_txdb0))

## -----------------------
## --- Ensembl Metazoa ---

## The metazoa mart is slow and at the same time it doesn't seem to
## support requests that take more than 1 min at the moment. So a call to
## biomaRt::getBM() will fail with a "Timeout was reached" error if the
## requested data takes more than 1 min to download. This unfortunately
## happens with the example below so we don't try to run it for now.

## Not run: 
  mart <- useMart(biomart="metazoa_mart", host="metazoa.ensembl.org")
  datasets <- listDatasets(mart)
  datasets$dataset
  worm_txdb <- makeTxDbFromBiomart(biomart="metazoa_mart",
                                   dataset="celegans_eg_gene",
                                   host="metazoa.ensembl.org")
  worm_txdb

  ## Note that even if the dataset for Worm on Ensembl Metazoa contains
  ## the same transcript as on the main Ensembl database, the transcript
  ## type might be annotated with slightly different terms (e.g. antisense
  ## vs antisense_RNA):
  filter <- list(tx_name="Y71G12B.44")
  transcripts(worm_txdb, filter=filter, columns=c("tx_name", "tx_type"))
  transcripts(txdb1, filter=filter, columns=c("tx_name", "tx_type"))

## End(Not run)
## ----------------------
## --- Ensembl Plants ---

## Like the metazoa mart (see above), the plants mart is also slow and
## doesn't seem to support requests that take more than 1 min either.
## So we don't try to run the example below for now.

## Not run: 
mart <- useMart(biomart="plants_mart", host="plants.ensembl.org")
datasets <- listDatasets(mart)
datasets[ , 1:2]
athaliana_txdb <- makeTxDbFromBiomart(biomart="plants_mart",
                                      dataset="athaliana_eg_gene",
                                      host="plants.ensembl.org")
athaliana_txdb

## End(Not run)
## ------------------------
## --- Ensembl Protists ---

mart <- useMart(biomart="protists_mart", host="protists.ensembl.org")
datasets <- listDatasets(mart)
datasets$dataset
tgondii_txdb <- makeTxDbFromBiomart(biomart="protists_mart",
                                    dataset="tgondii_eg_gene",
                                    host="protists.ensembl.org")
tgondii_txdb

## ---------------------------------------------------------------------
## C. USING AN Ensembl MIRROR
## ---------------------------------------------------------------------

## You can use the 'host' argument to access the "ENSEMBL_MART_ENSEMBL"
## BioMart database at a mirror (e.g. at 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:
if (interactive()) {
  txdb3 <- makeTxDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL",
                               dataset="hsapiens_gene_ensembl",
                               transcript_ids=transcript_ids,
                               host="useast.ensembl.org")
  txdb3
}

## ---------------------------------------------------------------------
## D. 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")

if (interactive()) {
  txdb4 <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl",
                               filter=my_filter)
  txdb4
  transcripts(txdb4, columns=c("tx_id", "tx_name", "gene_id"))
  transcriptLengths(txdb4)
}

## ---------------------------------------------------------------------
## E. RETRIEVING CHROMOSOME INFORMATION ONLY
## ---------------------------------------------------------------------

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

jmacdon/GenomicFeatures documentation built on Jan. 2, 2022, 7:40 a.m.