AnnotationDbi: Annotation Database Interface

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Provides user interface and database connection code for annotation data packages using SQLite data storage.

Author
Herve Pages, Marc Carlson, Seth Falcon, Nianhua Li
Date of publication
None
Maintainer
Bioconductor Package Maintainer <maintainer@bioconductor.org>
License
Artistic-2.0
Version
1.36.0

View on Bioconductor

Man pages

AnnDbObj-class
AnnDbObj objects
AnnDbPkg-checker
Check the SQL data contained in an SQLite-based annotation...
AnnotationDb-class
AnnotationDb objects and their progeny, methods etc.
AnnotationDbi-internals
AnnotationDbi internals
Bimap
Bimap objects and the Bimap interface
Bimap-direction
Methods for getting/setting the direction of a Bimap object,...
Bimap-envirAPI
Environment-like API for Bimap objects
BimapFiltering
Methods for getting/setting the filters on a Bimap object
BimapFormatting
Formatting a Bimap as a list or character vector
Bimap-keys
Methods for manipulating the keys of a Bimap object
Bimap-toTable
Methods for manipulating a Bimap object in a data-frame style
colsAndKeytypes
Descriptions of available values for 'columns' and...
createSimpleBimap
Creates a simple Bimap from a SQLite database in an situation...
GOColsAndKeytypes
Descriptions of available values for 'columns' and 'keytypes'...
GOFrame
GOFrame and GOAllFrame objects
GOTerms-class
Class "GOTerms"
InparanoidColsAndKeytypes
Descriptions of available values for 'columns' and 'keytypes'...
inpIDMapper
Convenience functions for mapping IDs through an appropriate...
KEGGFrame
KEGGFrame objects
make_eg_to_go_map
Create GO to Entrez Gene maps for chip-based packages
makeGOGraph
A convenience function to generate graphs based on the GO.db...
print.probetable
Print method for probetable objects
toSQLStringSet
Convert a vector to a quoted string for use as a SQL value...
unlist2
A replacement for unlist() that does not mangle the names

Files in this package

AnnotationDbi/DESCRIPTION
AnnotationDbi/NAMESPACE
AnnotationDbi/NEWS
AnnotationDbi/R
AnnotationDbi/R/00RTobjs.R
AnnotationDbi/R/AllClasses.R
AnnotationDbi/R/AllGenerics.R
AnnotationDbi/R/AnnDbObj-lowAPI.R
AnnotationDbi/R/AnnDbPkg-checker.R
AnnotationDbi/R/AnnDbPkg-templates-common.R
AnnotationDbi/R/Bimap-envirAPI.R
AnnotationDbi/R/Bimap.R
AnnotationDbi/R/BimapFormatting.R
AnnotationDbi/R/FlatBimap.R
AnnotationDbi/R/GOTerms.R
AnnotationDbi/R/SQL.R
AnnotationDbi/R/createAnnObjs-utils.R
AnnotationDbi/R/createAnnObjs.ARABIDOPSISCHIP_DB.R
AnnotationDbi/R/createAnnObjs.ARABIDOPSIS_DB.R
AnnotationDbi/R/createAnnObjs.COELICOLOR_DB.R
AnnotationDbi/R/createAnnObjs.GO_DB.R
AnnotationDbi/R/createAnnObjs.INPARANOID_DB.R
AnnotationDbi/R/createAnnObjs.KEGG_DB.R
AnnotationDbi/R/createAnnObjs.MALARIA_DB.R
AnnotationDbi/R/createAnnObjs.NCBICHIP_DBs.R
AnnotationDbi/R/createAnnObjs.NCBIORG_DBs.R
AnnotationDbi/R/createAnnObjs.ORGANISM_DB.R
AnnotationDbi/R/createAnnObjs.PFAM_DB.R
AnnotationDbi/R/createAnnObjs.YEASTCHIP_DB.R
AnnotationDbi/R/createAnnObjs.YEASTNCBI_DB.R
AnnotationDbi/R/createAnnObjs.YEAST_DB.R
AnnotationDbi/R/flatten.R
AnnotationDbi/R/inpIDMapper.R
AnnotationDbi/R/loadDb.R
AnnotationDbi/R/makeMap.R
AnnotationDbi/R/methods-AnnotationDb.R
AnnotationDbi/R/methods-Inparanoid.R
AnnotationDbi/R/methods-Inparanoid8.R
AnnotationDbi/R/methods-ReactomeDb.R
AnnotationDbi/R/methods-SQLiteConnection.R
AnnotationDbi/R/methods-geneCentricDbs-keys.R
AnnotationDbi/R/methods-geneCentricDbs.R
AnnotationDbi/R/print.probetable.R
AnnotationDbi/R/test_AnnotationDbi_package.R
AnnotationDbi/R/unlist2.R
AnnotationDbi/build
AnnotationDbi/build/vignette.rds
AnnotationDbi/inst
AnnotationDbi/inst/DBschemas
AnnotationDbi/inst/DBschemas/SchemaGuidelines.txt
AnnotationDbi/inst/DBschemas/schemas_0.9
AnnotationDbi/inst/DBschemas/schemas_0.9/00README.TXT
AnnotationDbi/inst/DBschemas/schemas_0.9/ARABIDOPSISCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_0.9/DataTypes.txt
AnnotationDbi/inst/DBschemas/schemas_0.9/FLYCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_0.9/FLY_DB.sql
AnnotationDbi/inst/DBschemas/schemas_0.9/GO_DB.sql
AnnotationDbi/inst/DBschemas/schemas_0.9/HUMANCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_0.9/HUMAN_DB.sql
AnnotationDbi/inst/DBschemas/schemas_0.9/KEGG_DB.sql
AnnotationDbi/inst/DBschemas/schemas_0.9/RODENTCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_0.9/RODENT_DB.sql
AnnotationDbi/inst/DBschemas/schemas_0.9/YEASTCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_0.9/YEAST_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0
AnnotationDbi/inst/DBschemas/schemas_1.0/00README.TXT
AnnotationDbi/inst/DBschemas/schemas_1.0/ARABIDOPSISCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/BOVINECHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/BOVINE_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/CANINECHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/CANINE_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/CHICKENCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/CHICKEN_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/DataTypes.txt
AnnotationDbi/inst/DBschemas/schemas_1.0/ECOLICHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/ECOLI_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/FLYCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/FLY_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/GO_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/HUMANCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/HUMANCROSSCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/HUMAN_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/INPARANOIDDROME_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/INPARANOIDHOMSA_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/INPARANOIDMUSMU_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/INPARANOIDRATNO_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/INPARANOIDSACCE_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/KEGG_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/MALARIA_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/MOUSECHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/MOUSE_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/PFAM_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/PIGCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/PIG_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/RATCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/RAT_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/WORMCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/WORM_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/YEASTCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/YEAST_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/ZEBRAFISHCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_1.0/ZEBRAFISH_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0
AnnotationDbi/inst/DBschemas/schemas_2.0/00README.TXT
AnnotationDbi/inst/DBschemas/schemas_2.0/ANOPHELES_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/ARABIDOPSISCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/ARABIDOPSIS_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/BOVINECHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/BOVINE_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/CANINECHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/CANINE_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/CHICKENCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/CHICKEN_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/CHIMP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/DataTypes.txt
AnnotationDbi/inst/DBschemas/schemas_2.0/ECOLI_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/FLYCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/FLY_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/GO_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/HUMANCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/HUMAN_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/INPARANOID_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/KEGG_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/MALARIA_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/MOUSECHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/MOUSE_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/PFAM_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/PIG_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/RATCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/RAT_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/RHESUS_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/WORMCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/WORM_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/XENOPUSCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/XENOPUS_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/YEASTCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/YEAST_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/ZEBRAFISHCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.0/ZEBRAFISH_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1
AnnotationDbi/inst/DBschemas/schemas_2.1/00README.TXT
AnnotationDbi/inst/DBschemas/schemas_2.1/ANOPHELES_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/ARABIDOPSISCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/ARABIDOPSIS_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/BOVINECHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/BOVINE_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/CANINECHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/CANINE_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/CHICKENCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/CHICKEN_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/CHIMP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/COELICOLOR_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/DataTypes.txt
AnnotationDbi/inst/DBschemas/schemas_2.1/ECOLI_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/FLYCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/FLY_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/GO_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/HUMANCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/HUMAN_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/INPARANOID_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/KEGG_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/MALARIA_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/MOUSECHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/MOUSE_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/PFAM_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/PIG_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/RATCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/RAT_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/RHESUS_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/WORMCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/WORM_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/XENOPUSCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/XENOPUS_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/YEASTCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/YEAST_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/ZEBRAFISHCHIP_DB.sql
AnnotationDbi/inst/DBschemas/schemas_2.1/ZEBRAFISH_DB.sql
AnnotationDbi/inst/NOTES-Herve
AnnotationDbi/inst/TODO
AnnotationDbi/inst/doc
AnnotationDbi/inst/doc/AnnotationDbi.R
AnnotationDbi/inst/doc/AnnotationDbi.Rnw
AnnotationDbi/inst/doc/AnnotationDbi.pdf
AnnotationDbi/inst/doc/IntroToAnnotationPackages.R
AnnotationDbi/inst/doc/IntroToAnnotationPackages.Rnw
AnnotationDbi/inst/doc/IntroToAnnotationPackages.pdf
AnnotationDbi/inst/extdata
AnnotationDbi/inst/extdata/HG-U95Av2_probe_tab.gz
AnnotationDbi/inst/extdata/Inp_species_mapping
AnnotationDbi/inst/extdata/hcg110_ID
AnnotationDbi/inst/extdata/hgu95av2_ID
AnnotationDbi/inst/extdata/manyToOneBlackList.Rda
AnnotationDbi/inst/extdata/org.testing.db
AnnotationDbi/inst/extdata/org.testing.db/DESCRIPTION
AnnotationDbi/inst/extdata/org.testing.db/NAMESPACE
AnnotationDbi/inst/extdata/org.testing.db/R
AnnotationDbi/inst/extdata/org.testing.db/R/zzz.R
AnnotationDbi/inst/extdata/org.testing.db/inst
AnnotationDbi/inst/extdata/org.testing.db/inst/extdata
AnnotationDbi/inst/extdata/org.testing.db/inst/extdata/org.testing.sqlite
AnnotationDbi/inst/extdata/org.testing.db/man
AnnotationDbi/inst/extdata/org.testing.db/man/org.TguttataTestingSubset.egBASE.Rd
AnnotationDbi/inst/extdata/org.testing.db/man/org.TguttataTestingSubset.egORGANISM.Rd
AnnotationDbi/inst/extdata/org.testing.db/man/org.TguttataTestingSubset.eg_dbconn.Rd
AnnotationDbi/inst/extdata/resultTable.Rda
AnnotationDbi/inst/script
AnnotationDbi/inst/script/generateMultiCols.R
AnnotationDbi/inst/unitTests
AnnotationDbi/inst/unitTests/test_bimap.R
AnnotationDbi/inst/unitTests/test_geneCentricDbs.R
AnnotationDbi/inst/unitTests/test_mapIds.R
AnnotationDbi/inst/unitTests/test_select.R
AnnotationDbi/inst/unitTests/test_select_NOSCHEMA.R
AnnotationDbi/inst/unitTests/test_select_inparanoid.R
AnnotationDbi/inst/unitTests/test_select_reactome.R
AnnotationDbi/man
AnnotationDbi/man/AnnDbObj-class.Rd
AnnotationDbi/man/AnnDbPkg-checker.Rd
AnnotationDbi/man/AnnotationDb-class.Rd
AnnotationDbi/man/AnnotationDbi-internals.Rd
AnnotationDbi/man/Bimap-direction.Rd
AnnotationDbi/man/Bimap-envirAPI.Rd
AnnotationDbi/man/Bimap-keys.Rd
AnnotationDbi/man/Bimap-toTable.Rd
AnnotationDbi/man/Bimap.Rd
AnnotationDbi/man/BimapFiltering.Rd
AnnotationDbi/man/BimapFormatting.Rd
AnnotationDbi/man/GOColsAndKeytypes.Rd
AnnotationDbi/man/GOFrame.Rd
AnnotationDbi/man/GOTerms-class.Rd
AnnotationDbi/man/InparanoidColsAndKeytypes.Rd
AnnotationDbi/man/KEGGFrame.Rd
AnnotationDbi/man/colsAndKeytypes.Rd
AnnotationDbi/man/createSimpleBimap.Rd
AnnotationDbi/man/inpIDMapper.Rd
AnnotationDbi/man/makeGOGraph.Rd
AnnotationDbi/man/make_eg_to_go_map.Rd
AnnotationDbi/man/print.probetable.Rd
AnnotationDbi/man/toSQLStringSet.Rd
AnnotationDbi/man/unlist2.Rd
AnnotationDbi/tests
AnnotationDbi/tests/AnnotationDbi_unit_tests.R
AnnotationDbi/vignettes
AnnotationDbi/vignettes/AnnotationDbi.Rnw
AnnotationDbi/vignettes/IntroToAnnotationPackages.Rnw
AnnotationDbi/vignettes/databaseTypes.pdf