Code for Building Annotation Database Packages

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Documentation for package ‘AnnotationForge’ version 1.10.1

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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
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
makeChipPackage Making a chip package from annotations available from data.frame of probes mapped to gene IDs and an existing org package.
makeDBPackage Creates a sqlite database, and then makes an annotation package with it
makeInpDb Builds an individual DB from online files at inparanoid that is in turn meant for generating Inparanoid 8 based objects.
makeOrgPackage Making an organism package from annotations available from a set of named data.frames.
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