Retrieve Ensembl Biomart marts and datasets for a query organism
Source:R/organismBM.R
organismBM.RdThis function returns either all available biomart connections for all available organisms for which biomart access is possible, or (when specified) returns all organism specific biomart connections.
Arguments
- organism
a character string specifying the scientific name of a query organism. Default is
organism=NULL. In this case all available biomart connections are returned.- update
a logical value specifying whether or not the local listMart.txt and listDatasets.txt files shall be updated by remote access to BioMart.
- mute_citation
logical value indicating whether citation message should be muted.
Details
This function collects all available biomart connections and returns a table storing the organism for which biomart connections are available as well as the corresponding mart and database.
Note
When you run this function for the first time, the data retrieval procedure
will take some time, due to the remote access to BioMart. The corresponding
result is then saved in a *.txt file named "_biomart/listDatasets.txt" in the
tempdir directory, allowing subsequent queries to perform
much faster.
References
Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Steffen Durinck, Paul T. Spellman, Ewan Birney and Wolfgang Huber, Nature Protocols 4, 1184-1191 (2009).
BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Steffen Durinck, Yves Moreau, Arek Kasprzyk, Sean Davis, Bart De Moor, Alvis Brazma and Wolfgang Huber, Bioinformatics 21, 3439-3440 (2005).
See also
Other biomaRt:
biomart(),
getAttributes(),
getDatasets(),
getMarts(),
organismFilters()
Examples
if (FALSE) { # \dontrun{
# returning all available biomart connections
head(organismBM(), 20)
# retrieving all available datasets and biomart connections for
# a specific query organism (scientific name)
organismBM(organism = "Homo sapiens")
# you can also update the downloaded version using
# the "update = TRUE" argument
head(organismBM(update = TRUE), 20)
} # }