CHANGES IN VERSION 1.16 ----------------------- NEW FEATURES o New Object types: Org.Db, ChipDb, GODb. These are loaded when an Annotation package is loaded. o select method for these new objects to extract data.frames of available annotations. Users can specify keys, along with the keytype, and the columns of data that they want extracted from the annotation package. o keys now will operate on new objects to expose most ID types as keys o keytypes will show which kinds of IDs can be used as a key by select o cols will display the kinds of data that can be extracted by select o Users who need organism packages for organisms that are annotated at NCBI can now use makeOrgPackageFromNCBI() to generate a basic organism package on the fly SIGNIFICANT USER-VISIBLE CHANGES o New objects are always named after the package that loaded them. So if you just loaded the hgu95av2.db package, your ChipDb object will be called hgu95av2.db o new fields are now required in the metadata table of annotation packages to allow the on-the-fly creation of these new objects. If you are constructing a custom package and want to extend this infrastructure, you may need to add some fields to the metadata table. BUG FIXES o makeProbePackage, and other generated Annotation packages have had templates modified so that packages can load and also to enable loading of new objects to allow new features in this release. o updated GOFrame constructor to allow use of new types of evidence codes. o generated packages will create databases with the appropiate metadata entries for the new objects.