AnnotationDbi v1.28.2
Annotation Database Interface
Provides user interface and database connection code
for annotation data packages using SQLite data storage.
Functions in AnnotationDbi
| Name | Description | |
| BimapFormatting | Formatting a Bimap as a list or character vector | |
| ACCNUM | Descriptions of available values for columns and keytypes. | |
| 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 package | |
| Bimap-direction | Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys | |
| Bimap-envirAPI | Environment-like API for Bimap objects | |
| inpIDMapper | Convenience functions for mapping IDs through an appropriate set of annotation packages | |
| KEGGFrame | KEGGFrame objects | |
| AnnDbPkg-checker | Check the SQL data contained in an SQLite-based annotation package | |
| createSimpleBimap | Creates a simple Bimap from a SQLite database in an situation that is external to AnnotationDbi | |
| AnnDbObj-objects | AnnDbObj objects | |
| AnnotationDbi-defunct | Defunct Functions in package AnnotationDbi | |
| unlist2 | A replacement for unlist() that does not mangle the names | |
| Bimap-keys | Methods for manipulating the keys of a Bimap object | |
| Bimap-toTable | Methods for manipulating a Bimap object in a data-frame style | |
| GOTerms-class | Class "GOTerms" | |
| HOMO_SAPIENS | Descriptions of available values for columns and keytypes for inparanpoid packages. | |
| Bimap | Bimap objects and the Bimap interface | |
| print.probetable | Print method for probetable objects | |
| toggleProbes | Methods for getting/setting the filters on a Bimap object | |
| toSQLStringSet | Convert a vector to a quoted string for use as a SQL value list | |
| GOID | Descriptions of available values for columns and keytypes for GO.db. | |
| AnnotationDb-objects | AnnotationDb objects and their progeny, methods etc. | |
| AnnotationDbi internals | AnnotationDbi internals | |
| GOFrame | GOFrame and GOAllFrame objects | |
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Details
| Collate | 00RTobjs.R unlist2.R AllGenerics.R AllClasses.R FlatBimap.R SQL.R AnnDbObj-lowAPI.R Bimap.R GOTerms.R BimapFormatting.R Bimap-envirAPI.R flatten.R methods-AnnotationDb.R methods-seqnames.R methods-geneCentricDbs.R methods-ReactomeDb.R methods-Inparanoid.R methods-Inparanoid8.R loadDb.R createAnnObjs-utils.R createAnnObjs.NCBIORG_DBs.R createAnnObjs.NCBICHIP_DBs.R createAnnObjs.ORGANISM_DB.R createAnnObjs.YEASTCHIP_DB.R createAnnObjs.COELICOLOR_DB.R createAnnObjs.ARABIDOPSISCHIP_DB.R createAnnObjs.MALARIA_DB.R createAnnObjs.YEAST_DB.R createAnnObjs.YEASTNCBI_DB.R createAnnObjs.ARABIDOPSIS_DB.R createAnnObjs.GO_DB.R createAnnObjs.KEGG_DB.R createAnnObjs.INPARANOID_DB.R createAnnObjs.PFAM_DB.R AnnDbPkg-templates-common.R AnnDbPkg-checker.R print.probetable.R makeMap.R inpIDMapper.R test_AnnotationDbi_package.R |
| License | Artistic-2.0 |
| biocViews | Annotation, Microarray, Sequencing, GenomeAnnotation |
| VignetteBuilder | knitr |
| Packaged | 2014-05-16 20:58:15 UTC; mcarlson |
| Video | https://www.youtube.com/watch?v=8qvGNTVz3Ik |
| suggests | AnnotationForge , BiocStyle , GO.db , graph , hgu95av2.db , hom.Hs.inp.db , KEGG.db , knitr , org.At.tair.db , org.Hs.eg.db , org.Sc.sgd.db , org.TguttataTestingSubset.eg.db , reactome.db , RUnit , TxDb.Hsapiens.UCSC.hg19.knownGene |
| depends | Biobase (>= 1.17.0) , BiocGenerics (>= 0.11.2) , methods , R (>= 2.7.0) , stats4 , utils |
| imports | DBI , RSQLite , S4Vectors |
| Contributors | Marc Carlson, Herve Pages, Nianhua Li, Seth Falcon |
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