Interface to BioMart databases (e.g. Ensembl, Wormbase and Gramene)


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Documentation for package ‘biomaRt’ version 1.16.0

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attributeSummary Gives a summary of the attributes groups and categories
exportFASTA Exports getSequence results to FASTA format
filterOptions Displays the filter options
filterSummary Gives a summary of the filters groups and categories
filterType Displays the filter type
getAffyArrays Displays affy identifiers of Affymetrix chips supported by the Ensembl package
getBM Retrieves information from the BioMart database
getGene Retrieves gene annotation information given a vector of identifiers
getGO Retrieves GO information
getHomolog Get homologs
getLDS Retrieves information from two linked datasets
getSequence Retrieves sequences
getSNP Retrieves SNP's between a given chromosome start and end position
listAttributes lists the attributes available in the selected dataset
listDatasets lists the datasets available in the selected BioMart database
listFilters lists the filters available in the selected dataset
listMarts lists the avilable BioMart databases
Mart-class Class Mart
martDisconnect Disconnects from BioMarts
parseAttributes parse attributes
parseFilters parse filters
show,Mart-method Class Mart
useDataset Select a dataset to use and updates Mart object
useMart Connects to the selected BioMart database and dataset