Code for Building Annotation Database Packages

[Up] [Top]

Documentation for package ‘AnnotationForge’ version 1.2.2

Help Pages

AnnDbPkg-maker Creates an SQLite-based annotation package
AnnDbPkgSeed Creates an SQLite-based annotation package
AnnDbPkgSeed-class Creates an SQLite-based annotation package
available.chipdbschemas available.db0pkgs
available.db0pkgs available.db0pkgs
available.dbschemas available.db0pkgs
class:AnnDbPkgSeed Creates an SQLite-based annotation package
createSimpleBimap Creates a simple Bimap from a SQLite database in an situation that is external to AnnotationDbi
generateSeqnames.db Generates the seqnames.db package and database
getProbeDataAffy Read a data file describing the probe sequences on an Affymetrix genechip
getProbeData_1lq Read a 1lq file for an Affymetrix genechip
loadAnnDbPkgIndex Creates an SQLite-based annotation package
makeAnnDbPkg Creates an SQLite-based annotation package
makeAnnDbPkg-method Creates an SQLite-based annotation package
makeDBPackage Creates a sqlite database, and then makes an annotation package with it
makeOrgPackageFromBiomart Making an organism package from annotations available from NCBI.
makeOrgPackageFromNCBI Making an organism package from annotations available from NCBI.
makeProbePackage Make a package with probe sequence related data for microarrays
popBOVINECHIPDB Populates an SQLite DB with and produces a schema definition
popBOVINEDB Populates an SQLite DB with and produces a schema definition
popCANINECHIPDB Populates an SQLite DB with and produces a schema definition
popCANINEDB Populates an SQLite DB with and produces a schema definition
popCHICKENCHIPDB Populates an SQLite DB with and produces a schema definition
popCHICKENDB Populates an SQLite DB with and produces a schema definition
popECOLICHIPDB Populates an SQLite DB with and produces a schema definition
popECOLIDB Populates an SQLite DB with and produces a schema definition
popFLYCHIPDB Populates an SQLite DB with and produces a schema definition
popFLYDB Populates an SQLite DB with and produces a schema definition
popHUMANCHIPDB Populates an SQLite DB with and produces a schema definition
popHUMANDB Populates an SQLite DB with and produces a schema definition
popMALARIADB Populates an SQLite DB with and produces a schema definition
popMOUSECHIPDB Populates an SQLite DB with and produces a schema definition
popMOUSEDB Populates an SQLite DB with and produces a schema definition
popPIGCHIPDB Populates an SQLite DB with and produces a schema definition
popPIGDB Populates an SQLite DB with and produces a schema definition
popRATCHIPDB Populates an SQLite DB with and produces a schema definition
popRATDB Populates an SQLite DB with and produces a schema definition
populateDB Populates an SQLite DB with and produces a schema definition
popWORMCHIPDB Populates an SQLite DB with and produces a schema definition
popWORMDB Populates an SQLite DB with and produces a schema definition
popYEASTDB Populates an SQLite DB with and produces a schema definition
popYEASTNCBIDB Populates an SQLite DB with and produces a schema definition
popZEBRAFISHCHIPDB Populates an SQLite DB with and produces a schema definition
popZEBRAFISHDB Populates an SQLite DB with and produces a schema definition
wrapBaseDBPackages Wrap up all the Base Databases into Packages for distribution