Package index • biomaRt

`Mart` class and methods

show(<Mart>): Class Mart

keys(<Mart>) keytypes(<Mart>) columns(<Mart>) select(<Mart>): Retrieve information from the BioMart databases

Create or update `Mart` objects

listMarts(): lists the available BioMart databases

listEnsembl() listEnsemblGenomes(): lists the available BioMart databases hosted by Ensembl

listEnsemblArchives(): Lists the available archived versions of Ensembl

useDataset(): Select a dataset to use and updates Mart object

useEnsembl() useEnsemblGenomes(): Connects to the selected BioMart database and dataset hosted by Ensembl

useMart(): Connects to the selected BioMart database and dataset

Extract data from BioMart databases

listAttributes() searchAttributes(): lists the attributes available in the selected dataset

attributePages(): Gives a summary of the attribute pages

listDatasets() searchDatasets(): List or search the datasets available in the selected BioMart database

listFilters() searchFilters(): List or search the filters available in the selected dataset

searchFilterOptions() listFilterOptions(): List or search the options available for a specified filter.

filterType(): Displays the filter type

getBM(): Retrieves information from the BioMart database

getGene(): Retrieves gene annotation information given a vector of identifiers

getHomologs(): List homologous genes between two species.

getLDS(): Retrieves information from two linked datasets

getSequence(): Retrieves sequences

Data export

exportFASTA(): Exports getSequence results to FASTA format

Network and cache utilities

setEnsemblSSL(): Save system specific SSL settings for contacting Ensembl

biomartCacheClear() biomartCacheInfo(): biomaRt result caching

Dataset

NP2009code(): Display the analysis code from the 2009 Nature protocols paper

Deprecated of Defunct functions

biomaRt-deprecated filterOptions searchFilterValues listFilterValues: Deprecated and defunct functions in package biomaRt