In addition to the
this function returns all available attributes that can be accessed through
different marts and datasets for a given query organism.
a character string specifying the scientific name of a query organism.
a logical value specifying whether or not the local listMart.txt, listDatasets.txt, and listAttributes_organism.txt files shall be updated by remote access to BioMart.
a character string specifying a topic (category) of attributes,
For a given query organism, this function retrieves all available attributes that can be accessed through different marts and datasets.
Sometimes the same attribute 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 attributes.
topic argument allows the user to search for specific attribute
topics/categories for faster filtering.
a data.frame storing corresponding attribute names, description, datasets, and marts.
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
directory named "_biomart/listMarts.txt","_biomart/listDatasets.txt", and
"_biomart/listAttributes_organism.txt", allowing subsequent queries to
perform much faster.
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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