This 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.
a character string specifying the scientific name of a
query organism. Default is
a logical value specifying whether or not the local listMart.txt and listDatasets.txt files shall be updated by remote access to BioMart.
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.
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
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).
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## Not run: # 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) ## End(Not run)
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