Package index • BED

All functions

BED: Biological Entity Dictionary (BED)

BEIDList(): Create a BEIDList

BEIDs(): Get the BEIDs from an object

beIDsToAllScopes(): Find all BEID and ProbeID corresponding to a BE

bedCall(): Call a function on the BED graph

bedImport(): Feeding BED: Imports a data.frame in the BED graph database

beidsServer() beidsUI(): Shiny module for searching BEIDs

cacheBedCall(): Cached neo4j call

cacheBedResult(): Put a BED query result in cache

checkBeIds(): Check biological entities (BE) identifiers

checkBedCache(): Check BED cache

checkBedConn(): Check if there is a connection to a BED database

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(<BEIDList>): Convert a BEIDList object in a specific identifier (BEID) scope

focusOnScope(): Focus a BE related object on a specific identifier (BEID) scope

forgetBedConnection(): Forget a BED connection

genBePath(): Construct CQL sub-query to map 2 biological entity

genProbePath(): Identify the biological entity (BE) targeted by probes and construct the CQL sub-query to map probes to the BE

geneIDsToAllScopes(): Find all GeneID, ObjectID, TranscriptID, PeptideID and ProbeID corresponding to a Gene in any organism

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

getBeIdNameTable(): Get a table of biological entity (BE) identifiers and names

getBeIdNames(): Get names of Biological Entity identifiers

getBeIdSymbolTable(): Get a table of biological entity (BE) identifiers and symbols

getBeIdSymbols(): Get symbols of Biological Entity identifiers

getBeIdURL(): Get reference URLs for BE IDs

getBeIds(): Get biological entities identifiers

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

guessIdScope() guessIdOrigin(): 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

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

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

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<-`(): Set object metadata

metadata(): Get 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