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


[Package List] [Top]

Documentation for package `biomaRt' version 1.8.2

User Guides and Package Vignettes

Read overview or browse directory.

Help Pages

cleanBM Clear getBM result from duplicates
exportFASTA Exports getSequence results to FASTA format
getAffyArrays Displays affy identifiers of Affymetrix chips supported by the Ensembl package
getBM Retrieves information from the BioMart database
getFeature Retrieves Feature starting from a gene symbol and array identifier
getGene Retrieves Gene information
getGO Retrieves GO information
getHomolog Get homologs
getINTERPRO Retrieves INTERPRO protein domain information
getOMIM Retrieves OMIM information
getPossibleXrefs Get possible cross-references in Ensembl
getSequence Retrieves sequences
getSNP Retrieves SNP's between a given chromosome start and end position
getXref Get cross reference in Ensembl
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 list the BioMart database covered by biomaRt package
Mart-class Class Mart
martDisconnect Disconnects from BioMarts
martTable-class Class martTable
parseAttributes parse attributes
parseFilters parse filters
useDataset Select a dataset to use and updates Mart object
useMart Connects to the selected BioMart