Retrieve Ensembl Biomart filters for a query organism

In addition to the organismBM and organismAttributes functions, this function returns all available filters that can be accessed through different marts and datasets for a given query organism.

Usage

organismFilters(organism, update = FALSE, topic = NULL)

Arguments

organism

a character string specifying the scientific name of a query organism.

update

a logical value specifying whether or not the local listMart.txt, listDatasets.txt, and listFilters_organism.txt files shall be updated by remote access to BioMart.

topic

a character string specifying a topic (category) of filters, e.g. topic = "id".

Value

a data.frame storing corresponding filter names, description, datasets, and marts.

Details

For a given query organism, this function retrieves all available filters that can be accessed through different marts and datasets.

Sometimes the same filter names correspond to different datasets and marts causing problems when using getMarts. The approach introduced by this function provides (again) a organism centric way of accessing organism specific filters.

The topic argument allows the user to search for specific filters topics/categories for faster selection.

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 within the tempdir directory named "_biomart/listMarts.txt","_biomart/listDatasets.txt", and "_biomart/listFilters_organism.txt", allowing subsequent queries to perform much faster.

References

http://biomart.org/

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(), organismBM()

Author

Hajk-Georg Drost

Examples

if (FALSE) { # \dontrun{
# search for filter topic "id"
head(organismFilters("Homo sapiens", topic = "id"), 20)
} # }