Package: AnnotationDbi 1.69.0

Bioconductor Package Maintainer

AnnotationDbi: Manipulation of SQLite-based annotations in Bioconductor

Implements a user-friendly interface for querying SQLite-based annotation data packages.

Authors:Hervé Pagès, Marc Carlson, Seth Falcon, Nianhua Li

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AnnotationDbi.pdf |AnnotationDbi.html✨
AnnotationDbi/json (API)
NEWS

# 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-1.67.0(bioc 3.20)AnnotationDbi-1.66.0(bioc 3.19)

annotation microarray sequencing genomeannotation bioconductor-package core-package

14.16 score 9 stars 770 packages 3.2k scripts 67k downloads 106 exports 37 dependencies

Last updated 23 days agofrom:faea5ea106. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	WARNING	Oct 30 2024
R-4.5-linux	WARNING	Oct 30 2024
R-4.4-win	WARNING	Oct 30 2024
R-4.4-mac	WARNING	Oct 30 2024
R-4.3-win	WARNING	Oct 30 2024
R-4.3-mac	WARNING	Oct 30 2024

Exports:as.data.frame as.data.frame.Bimap as.list as.list.Bimap checkMAPCOUNTS chooseCentralOrgPkgSymbol colmetanames colnames columns contents count.links count.mappedkeys count.mappedLkeys count.mappedRkeys createAnnObjs.SchemaChoice createSimpleBimap dbconn dbfile dbFileConnect dbFileDisconnect dbGetTable dbInfo dbmeta dbschema debugSQL Definition direction direction<-eapply exists filterSeeds get getBimapFilters getGOFrameData getKEGGFrameData getOrgPkgForSchema GOAllFrame GOFrame GOID GOTerms hasMultiProbes hasSingleProbes head idConverter initialize inpIDMapper intraIDMapper isNA KEGGFrame keyname keys keys<-keytypes links Lkeyname Lkeys Lkeys<-Llength loadDb ls make_eg_to_go_map make_go_to_eg_map makeGOGraph mapIds mapIds_base mappedkeys mappedLkeys mappedRkeys mergeToNamespaceAndExport metadata mget NCBICHIP_DB_SeedGenerator ncol nhit nrow Ontology organismKEGGFrame orgPackageName Rattribnames Rattribnames<-resort_base revmap Rkeyname Rkeys Rkeys<-Rlength sample saveDb Secondary select show showQCData species subset summary Synonym tagname tail taxonomyId Term testForValidKeytype testSelectArgs toggleProbes toSQLStringSet toTable unlist2

Dependencies:askpass Biobase BiocGenerics Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI fastmap GenomeInfoDb GenomeInfoDbData glue httr IRanges jsonlite KEGGREST lifecycle memoise mime openssl pkgconfig plogr png R6 rlang RSQLite S4Vectors sys UCSC.utils vctrs XVector zlibbioc

Introduction To Bioconductor Annotation Packages

Rendered fromIntroToAnnotationPackages.Rnwusingknitr::knitron Oct 30 2024.

Last update: 2021-01-29
Started: 2013-10-22

(Deprecated) How to use bimaps from the ".db" annotation packages

Rendered fromAnnotationDbi.Rnwusingknitr::knitron Oct 30 2024.

Last update: 2019-03-05
Started: 2013-10-22

Citation

Development and contributors

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