AnnotationForge v1.10.1

Code for Building Annotation Database Packages

Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.

Functions in AnnotationForge

Name Description
makeOrgPackage Making an organism package from annotations available from a set of named data.frames.
getProbeData_1lq Read a 1lq file for an Affymetrix genechip
getProbeDataAffy Read a data file describing the probe sequences on an Affymetrix genechip
generateSeqnames.db Generates the seqnames.db package and database
makeProbePackage Make a package with probe sequence related data for microarrays
makeOrgPackageFromNCBI Making an organism package from annotations available from NCBI.
makeChipPackage Making a chip package from annotations available from data.frame of probes mapped to gene IDs and an existing org package.
makeInpDb Builds an individual DB from online files at inparanoid that is in turn meant for generating Inparanoid 8 based objects.
available.db0pkgs available.db0pkgs
AnnDbPkg-maker Creates an SQLite-based annotation package
makeDBPackage Creates a sqlite database, and then makes an annotation package with it
wrapBaseDBPackages Wrap up all the Base Databases into Packages for distribution
populateDB Populates an SQLite DB with and produces a schema definition
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Collate AnnDbPkg-maker.R sqlForge_utils.R sqlForge_baseMapBuilder.R sqlForge_schemaGen.R sqlForge_tableBuilder.R sqlForge_makeAnnPkgs.R sqlForge_wrapBaseDBPkgs.R sqlForge_seqnames.R makeProbePackage.R makeOrgPackageFromDataFrames.R makeChipPackageFromDataFrames.R NCBI_ftp.R NCBI_getters.R makeInparanoidDbs.R test_AnnotationForge_package.R
License Artistic-2.0
biocViews Annotation, Infrastructure
VignetteBuilder knitr

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