1 AnnotationDb objects and the select method | 2 ChipDb objects and the select method | 3 OrgDb objects and the select method | 4 Using select with GO.db | 5 Using select with TxDb packages | 6 Using select with EnsDb packages
Package: AnnotationDbi 1.75.0
Bioconductor Package Maintainer
AnnotationDbi: Manipulation of SQLite-based annotations in Bioconductor
Implements a user-friendly interface for querying SQLite-based annotation data packages.
Authors:
AnnotationDbi_1.75.0.tar.gz
AnnotationDbi_1.75.0.zip(r-4.7)AnnotationDbi_1.75.0.zip(r-4.6)AnnotationDbi_1.75.0.zip(r-4.5)
AnnotationDbi_1.75.0.tgz(r-4.6-any)AnnotationDbi_1.75.0.tgz(r-4.5-any)
AnnotationDbi_1.75.0.tar.gz(r-4.7-any)AnnotationDbi_1.75.0.tar.gz(r-4.6-any)
AnnotationDbi_1.75.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
AnnotationDbi/json (API)
| # Install 'AnnotationDbi' in R: |
| install.packages('AnnotationDbi', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bioconductor/annotationdbi/issues
On BioConductor:AnnotationDbi-1.75.0(bioc 3.24)AnnotationDbi-1.74.0(bioc 3.23)
annotationmicroarraysequencinggenomeannotationbioconductor-packagecore-package
Last updated from:59cd1dc7d8. Checks:8 ERROR, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 355 | ||
| linux-devel-x86_64 | ERROR | 466 | ||
| source / vignettes | OK | 438 | ||
| linux-release-x86_64 | ERROR | 527 | ||
| macos-release-arm64 | ERROR | 329 | ||
| macos-oldrel-arm64 | ERROR | 207 | ||
| windows-devel | ERROR | 735 | ||
| windows-release | ERROR | 711 | ||
| windows-oldrel | ERROR | 893 | ||
| wasm-release | OK | 323 |
Exports:as.data.frameas.data.frame.Bimapas.listas.list.BimapcheckMAPCOUNTSchooseCentralOrgPkgSymbolcolmetanamescolnamescolumnscontentscount.linkscount.mappedkeyscount.mappedLkeyscount.mappedRkeyscreateAnnObjs.SchemaChoicecreateSimpleBimapdbconndbfiledbFileConnectdbFileDisconnectdbGetTabledbInfodbmetadbschemadebugSQLDefinitiondirectiondirection<-eapplyexistsfilterSeedsgetgetBimapFiltersgetGOFrameDatagetKEGGFrameDatagetOrgPkgForSchemaGOAllFrameGOFrameGOIDGOTermshasMultiProbeshasSingleProbesheadidConverterinitializeinpIDMapperintraIDMapperisNAKEGGFramekeynamekeyskeys<-keytypeslinksLkeynameLkeysLkeys<-LlengthloadDblsmake_eg_to_go_mapmake_go_to_eg_mapmakeGOGraphmapIdsmapIds_basemappedkeysmappedLkeysmappedRkeysmergeToNamespaceAndExportmetadatamgetNCBICHIP_DB_SeedGeneratorncolnhitnrowOntologyorganismKEGGFrameorgPackageNameRattribnamesRattribnames<-resort_baserevmapRkeynameRkeysRkeys<-RlengthsamplesaveDbSecondaryselectshowshowQCDataspeciessubsetsummarySynonymtagnametailtaxonomyIdTermtestForValidKeytypetestSelectArgstoggleProbestoSQLStringSettoTableunlist2
Dependencies:askpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapgenericsgluehttrIRangesjsonliteKEGGRESTlifecyclememoisemimeopensslpkgconfigpngR6rlangRSQLiteS4VectorsSeqinfosysvctrsXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Descriptions of available values for 'columns' and 'keytypes'. | ACCNUM ALIAS ARACYC ARACYCENZYME CHR CHRLOC CHRLOCEND COMMON DESCRIPTION ENSEMBL ENSEMBLPROT ENSEMBLTRANS ENTREZID ENZYME EVIDENCE EVIDENCEALL GENENAME GO GOALL INTERPRO IPI MAP OMIM ONTOLOGYALL ORF PATH PFAM PMID PROBEID PROSITE REFSEQ SGD SMART SYMBOL TAIR UNIGENE UNIPROT |
| AnnDbObj objects | AnnDbObj AnnDbObj-class AnnDbObj-objects class:AnnDbObj dbconn dbconn,AnnDbObj-method dbconn,environment-method dbconn,SQLiteConnection-method dbfile dbfile,AnnDbObj-method dbfile,environment-method dbfile,SQLiteConnection-method dbInfo dbInfo,AnnDbObj-method dbInfo,DBIConnection-method dbInfo,environment-method dbmeta dbmeta,AnnDbObj-method dbmeta,DBIConnection-method dbmeta,environment-method dbschema dbschema,AnnDbObj-method dbschema,DBIConnection-method dbschema,environment-method |
| Check the SQL data contained in an SQLite-based annotation package | AnnDbPkg-checker checkMAPCOUNTS |
| AnnotationDb objects and their progeny, methods etc. | AnnotationDb AnnotationDb-class ChipDb-class class:AnnotationDb cols columns columns,AnnotationDb-method columns,ChipDb-method columns,GODb-method columns,Inparanoid8Db-method columns,InparanoidDb-method columns,OrgDb-method columns,OrthologyDb-method columns,ReactomeDb-method dbconn,AnnotationDb-method dbfile,AnnotationDb-method GODb-class InparanoidDb-class keys keys,ChipDb-method keys,GODb-method keys,Inparanoid8Db-method keys,InparanoidDb-method keys,OrgDb-method keys,OrthologyDb-method keys,ReactomeDb-method keytypes keytypes,ChipDb-method keytypes,GODb-method keytypes,Inparanoid8Db-method keytypes,InparanoidDb-method keytypes,OrgDb-method keytypes,OrthologyDb-method keytypes,ReactomeDb-method loadDb mapIds mapIds,AnnotationDb-method metadata,AnnotationDb-method names,AnnotationDb-method OrgDb-class OrthologyDb-class ReactomeDb-class saveDb saveDb,AnnotationDb-method select select,ChipDb-method select,GODb-method select,Inparanoid8Db-method select,InparanoidDb-method select,OrgDb-method select,OrthologyDb-method select,ReactomeDb-method show,AnnotationDb-method species species,AnnotationDb-method taxonomyId taxonomyId,AnnotationDb-method |
| Bimap objects and the Bimap interface | AgiAnnDbMap AgiAnnDbMap-class AnnDbBimap AnnDbBimap-class AnnDbMap AnnDbMap-class Bimap Bimap-class class:AgiAnnDbMap class:AnnDbBimap class:AnnDbMap class:Bimap class:Go3AnnDbBimap class:GoAnnDbBimap class:GOTermsAnnDbBimap class:IpiAnnDbMap class:ProbeAnnDbBimap class:ProbeAnnDbMap class:ProbeGo3AnnDbBimap class:ProbeIpiAnnDbMap Go3AnnDbBimap Go3AnnDbBimap-class GoAnnDbBimap GoAnnDbBimap-class GOTermsAnnDbBimap GOTermsAnnDbBimap-class IpiAnnDbMap IpiAnnDbMap-class ProbeAnnDbBimap ProbeAnnDbBimap-class ProbeAnnDbMap ProbeAnnDbMap-class ProbeGo3AnnDbBimap ProbeGo3AnnDbBimap-class ProbeIpiAnnDbMap ProbeIpiAnnDbMap-class show,AnnDbBimap-method show,FlatBimap-method summary,AnnDbBimap-method summary,Bimap-method |
| Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys | Bimap-direction count.mappedLkeys count.mappedLkeys,AgiAnnDbMap-method count.mappedLkeys,AnnDbBimap-method count.mappedLkeys,Bimap-method count.mappedLkeys,Go3AnnDbBimap-method count.mappedRkeys count.mappedRkeys,AnnDbBimap-method count.mappedRkeys,AnnDbMap-method count.mappedRkeys,Bimap-method count.mappedRkeys,Go3AnnDbBimap-method direction direction,AnnDbBimap-method direction,FlatBimap-method direction<- direction<-,AnnDbBimap-method direction<-,AnnDbMap-method direction<-,FlatBimap-method Lkeys Lkeys,AnnDbBimap-method Lkeys,FlatBimap-method Lkeys,ProbeAnnDbBimap-method Lkeys,ProbeAnnDbMap-method Lkeys,ProbeGo3AnnDbBimap-method Lkeys,ProbeIpiAnnDbMap-method Lkeys<- Lkeys<-,AnnDbBimap-method Lkeys<-,FlatBimap-method Llength Llength,AnnDbBimap-method Llength,Bimap-method Llength,ProbeAnnDbBimap-method Llength,ProbeAnnDbMap-method Llength,ProbeGo3AnnDbBimap-method Llength,ProbeIpiAnnDbMap-method mappedLkeys mappedLkeys,AgiAnnDbMap-method mappedLkeys,AnnDbBimap-method mappedLkeys,FlatBimap-method mappedLkeys,Go3AnnDbBimap-method mappedRkeys mappedRkeys,AnnDbBimap-method mappedRkeys,AnnDbMap-method mappedRkeys,FlatBimap-method mappedRkeys,Go3AnnDbBimap-method revmap revmap,AnnDbBimap-method revmap,Bimap-method revmap,environment-method revmap,list-method Rkeys Rkeys,AnnDbBimap-method Rkeys,AnnDbMap-method Rkeys,FlatBimap-method Rkeys,Go3AnnDbBimap-method Rkeys<- Rkeys<-,AnnDbBimap-method Rkeys<-,FlatBimap-method Rlength Rlength,AnnDbBimap-method Rlength,AnnDbMap-method Rlength,Bimap-method Rlength,Go3AnnDbBimap-method subset,AnnDbBimap-method subset,Bimap-method |
| Environment-like API for Bimap objects | $,Bimap-method Bimap-envirAPI contents,Bimap-method eapply eapply,Bimap-method exists exists,ANY,ANY,Bimap-method exists,ANY,Bimap,missing-method get get,ANY,ANY,Bimap-method get,ANY,Bimap,missing-method ls ls,Bimap-method mget mget,ANY,Bimap-method mget,Bimap-method sample sample,Bimap-method sample,environment-method [[,Bimap-method |
| Methods for manipulating the keys of a Bimap object | Bimap-keys count.mappedkeys count.mappedkeys,ANY-method count.mappedkeys,Bimap-method isNA isNA,ANY-method isNA,Bimap-method isNA,environment-method keys,Bimap-method keys<- keys<-,Bimap-method length,Bimap-method mappedkeys mappedkeys,Bimap-method mappedkeys,environment-method mappedkeys,vector-method show,AnnDbTable-method [,Bimap-method |
| Methods for manipulating a Bimap object in a data-frame style | as.data.frame,Bimap-method as.data.frame.Bimap Bimap-toTable colmetanames colmetanames,AnnDbBimap-method colmetanames,FlatBimap-method colnames colnames,AnnDbBimap-method colnames,FlatBimap-method count.links count.links,Bimap-method count.links,Go3AnnDbBimap-method dim,Bimap-method head,FlatBimap-method keyname keyname,Bimap-method links links,AnnDbBimap-method links,Bimap-method links,FlatBimap-method links,Go3AnnDbBimap-method Lkeyname Lkeyname,AnnDbBimap-method Lkeyname,Bimap-method ncol ncol,Bimap-method nhit nhit,Bimap-method nhit,environment-method nhit,list-method nrow nrow,AnnDbBimap-method nrow,AnnDbTable-method nrow,Bimap-method nrow,FlatBimap-method nrow,Go3AnnDbBimap-method Rattribnames Rattribnames,AnnDbBimap-method Rattribnames,Bimap-method Rattribnames<- Rattribnames<-,AnnDbBimap-method Rattribnames<-,FlatBimap-method Rattribnames<-,Go3AnnDbBimap-method Rkeyname Rkeyname,AnnDbBimap-method Rkeyname,Bimap-method tagname tagname,AnnDbBimap-method tagname,Bimap-method tail,FlatBimap-method toTable toTable,Bimap-method toTable,FlatBimap-method |
| Formatting a Bimap as a list or character vector | as.character,AnnDbBimap-method as.character,FlatBimap-method as.list as.list,AgiAnnDbMap-method as.list,Bimap-method as.list,FlatBimap-method as.list,GoAnnDbBimap-method as.list,GOTermsAnnDbBimap-method as.list,IpiAnnDbMap-method as.list.Bimap BimapFormatting |
| Creates a simple Bimap from a SQLite database in an situation that is external to AnnotationDbi | createSimpleBimap |
| GOFrame and GOAllFrame objects | class:GOAllFrame class:GOFrame getGOFrameData getGOFrameData,GOAllFrame-method getGOFrameData,GOFrame-method GOAllFrame GOAllFrame,GOFrame-method GOAllFrame-class GOFrame GOFrame,data.frame,character-method GOFrame,data.frame,missing-method GOFrame-class |
| Descriptions of available values for 'columns' and 'keytypes' for GO.db. | DEFINITION GOID ONTOLOGY TERM |
| Class "GOTerms" | class:GOTerms Definition Definition,character-method Definition,GOTerms-method Definition,GOTermsAnnDbBimap-method GOID,character-method GOID,GOTerms-method GOID,GOTermsAnnDbBimap-method GOTerms GOTerms-class initialize,GOTerms-method Ontology Ontology,character-method Ontology,GOTerms-method Ontology,GOTermsAnnDbBimap-method Secondary Secondary,character-method Secondary,GOTerms-method Secondary,GOTermsAnnDbBimap-method show,GOTerms-method Synonym Synonym,character-method Synonym,GOTerms-method Synonym,GOTermsAnnDbBimap-method Term Term,character-method Term,GOTerms-method Term,GOTermsAnnDbBimap-method |
| Convenience functions for mapping IDs through an appropriate set of annotation packages | idConverter inpIDMapper intraIDMapper |
| KEGGFrame objects | class:KEGGFrame getKEGGFrameData getKEGGFrameData,KEGGAllFrame-method getKEGGFrameData,KEGGFrame-method KEGGFrame KEGGFrame,data.frame,character-method KEGGFrame,data.frame,missing-method KEGGFrame-class |
| Create GO to Entrez Gene maps for chip-based packages | make_eg_to_go_map make_go_to_eg_map |
| A convenience function to generate graphs based on the GO.db package | makeGOGraph |
| A data frame that maps species names to KEGG organisms | organismKEGGFrame |
| Org package contained in annotation object | orgPackageName |
| Print method for probetable objects | print.probetable |
| Methods for getting/setting the filters on a Bimap object | getBimapFilters getBimapFilters,AnnDbBimap-method hasMultiProbes hasMultiProbes,ProbeAnnDbBimap-method hasMultiProbes,ProbeAnnDbMap-method hasMultiProbes,ProbeGo3AnnDbBimap-method hasMultiProbes,ProbeIpiAnnDbMap-method hasSingleProbes hasSingleProbes,ProbeAnnDbBimap-method hasSingleProbes,ProbeAnnDbMap-method hasSingleProbes,ProbeGo3AnnDbBimap-method hasSingleProbes,ProbeIpiAnnDbMap-method toggleProbes toggleProbes,ProbeAnnDbBimap-method toggleProbes,ProbeAnnDbMap-method toggleProbes,ProbeGo3AnnDbBimap-method toggleProbes,ProbeIpiAnnDbMap-method |
| Convert a vector to a quoted string for use as a SQL value list | toSQLStringSet |
| A replacement for unlist() that does not mangle the names | unlist2 |
