Biological Entity Dictionary (BED)

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Documentation for package ‘BED’ version 1.5.1

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BED Biological Entity Dictionary (BED)
bedCall Call a function on the BED graph
bedImport Feeding BED: Imports a data.frame in the BED graph database
BEIDList Create a BEIDList
BEIDs Get the BEIDs from an object
beidsServer Shiny module for searching BEIDs
beIDsToAllScopes Find all BEID and ProbeID corresponding to a BE
beidsUI Shiny module for searching BEIDs
cacheBedCall Cached neo4j call
cacheBedResult Put a BED query result in cache
checkBedCache Check BED cache
checkBedConn Check if there is a connection to a BED database
checkBeIds Check biological entities (BE) identifiers
cleanDubiousXRef Identify and remove dubious cross-references
clearBedCache Clear the BED cache SQLite database
compareBedInstances Compare 2 BED database instances
connectToBed Connect to a neo4j BED database
convBeIdLists Converts lists of BE IDs
convBeIds Converts BE IDs
convDfBeIds Add BE ID conversion to a data frame
dumpEnsCore Feeding BED: Dump table from the Ensembl core database
dumpNcbiDb Feeding BED: Dump tables from the NCBI gene DATA
dumpNcbiTax Feeding BED: Dump tables with taxonomic information from NCBI
dumpUniprotDb Feeding BED: Dump and preprocess flat data files from Uniprot
exploreBe Explore BE identifiers
exploreConvPath Explore the shortest convertion path between two identifiers
filterByBEID Filter an object to keep only a set of BEIDs
findBe Find Biological Entity
findBeids Find Biological Entity identifiers
firstCommonUpstreamBe First common upstream BE
focusOnScope Focus a BE related object on a specific identifier (BEID) scope
focusOnScope.BEIDList Convert a BEIDList object in a specific identifier (BEID) scope
forgetBedConnection Forget a BED connection
genBePath Construct CQL sub-query to map 2 biological entity
geneIDsToAllScopes Find all GeneID, ObjectID, TranscriptID, PeptideID and ProbeID corresponding to a Gene in any organism
genProbePath Identify the biological entity (BE) targeted by probes and construct the CQL sub-query to map probes to the BE
getAllBeIdSources List all the source databases of BE identifiers whatever the BE type
getBeIdConvTable Get a conversion table between biological entity (BE) identifiers
getBeIdDescription Get description of Biological Entity identifiers
getBeIdNames Get names of Biological Entity identifiers
getBeIdNameTable Get a table of biological entity (BE) identifiers and names
getBeIds Get biological entities identifiers
getBeIdSymbols Get symbols of Biological Entity identifiers
getBeIdSymbolTable Get a table of biological entity (BE) identifiers and symbols
getBeIdURL Get reference URLs for BE IDs
getDirectOrigin Get the direct origin of BE identifiers
getDirectProduct Get the direct product of BE identifiers
getEnsemblGeneIds Feeding BED: Download Ensembl DB and load gene information in BED
getEnsemblPeptideIds Feeding BED: Download Ensembl DB and load peptide information in BED
getEnsemblTranscriptIds Feeding BED: Download Ensembl DB and load transcript information in BED
getGeneDescription Get description of genes corresponding to Biological Entity identifiers
getHomTable Get gene homologs between 2 organisms
getNcbiGeneTransPep Feeding BED: Download NCBI gene DATA and load gene, transcript and peptide information in BED
getOrgNames Get organism names from taxonomy IDs
getRelevantIds Get relevant IDs for a formerly identified BE in a context of interest
getTargetedBe Identify the biological entity (BE) targeted by probes
getTaxId Get taxonomy ID of an organism name
getUniprot Feeding BED: Download Uniprot information in BED
guessIdOrigin Guess biological entity (BE), database source and organism of a vector of identifiers.
guessIdScope Guess biological entity (BE), database source and organism of a vector of identifiers.
identicalScopes Check if two objects have the same BEID scope
is.BEIDList Check if the provided object is a BEIDList
largestBeSource Autoselect source of biological entity identifiers
listBe Lists all the biological entities (BE) available in the BED database
listBeIdSources Lists all the databases taken into account in the BED database for a biological entity (BE)
listDBAttributes List all attributes provided by a BEDB
listOrganisms Lists all the organisms available in the BED database
listPlatforms Lists all the probe platforms available in the BED database
loadBE Feeding BED: Load biological entities in BED
loadBeAttribute Feeding BED: Load attributes for biological entities in BED
loadBedModel Feeding BED: Load BED data model in neo4j
loadBedOtherIndexes Feeding BED: Load additional indexes in neo4j
loadBedResult Get a BED query result from cache
loadBENames Feeding BED: Load names associated to BEIDs
loadBESymbols Feeding BED: Load symbols associated to BEIDs
loadBEVersion Feeding BED: Load biological entities in BED with information about DB version
loadCodesFor Feeding BED: Load correspondance between genes and objects as coding events
loadCorrespondsTo Feeding BED: Load correspondances between BE IDs
loadHistory Feeding BED: Load history of BEIDs
loadIsAssociatedTo Feeding BED: Load BE ID associations
loadIsExpressedAs Feeding BED: Load correspondance between genes and transcripts as expression events
loadIsHomologOf Feeding BED: Load homology between BE IDs
loadIsTranslatedIn Feeding BED: Load correspondance between transcripts and peptides as translation events
loadLuceneIndexes Feeding BED: Create Lucene indexes in neo4j
loadNCBIEntrezGOFunctions Feeding BED: Load in BED GO functions associated to Entrez gene IDs from NCBI
loadNcbiTax Feeding BED: Load taxonomic information from NCBI
loadOrganisms Feeding BED: Load organisms in BED
loadPlf Feeding BED: Load a probes platform
loadProbes Feeding BED: Load probes targeting BE IDs
lsBedCache List all the BED queries in cache and the total size of the cache
lsBedConnections List all registered BED connection
metadata Get object metadata
metadata<- Set object metadata
registerBEDB Feeding BED: Register a database of biological entities in BED DB
scope Get the BEID scope of an object
scopes Get the BEID scopes of an object
searchBeid Search a BEID
searchId Search identifier, symbol or name information
setBedVersion Feeding BED: Set the BED version
showBedDataModel Show the data model of BED