4.4 years ago by
So you have generated an annotation package and installed it into your library. Why do you now want to insert these other data into the database for your annotation package? Do you really need to do that? Because there are many immediate downsides to that approach, and there are other ways that you can preserve your custom data.
Regarding the data that you mentioned, there already exists a class of packages for storing probe position, and it seems like getting the sequence data for the probes could be extracted from a simple GRanges object combined with the appropriate BSgenome object.
I can also tell you that if you really need to use databases to store the data you have in mind, that AnnotationForge has tools that will let you (for example) make a custom OrgDb package from data.frames. And OrganismDbi allows you to use several different database objects together as if they were a single object (providing that they all implement a select() method). So if you have a situation where you have several different types of annotation databases, these resources can all work together in a modular fashion without having to define bimaps or do any of the things that are discussed in that really old document that Gabor created. So if you are really interested in exploring this kind of stuff I would recommend that you look at the following documents (as I fear you may have been reading some very old files - based on your mentioning the Gabor document):
For a more current overview of the annotation resources:
For information about OrganismDbi:
And from AnnotationForge you should look at the help page for the makeOrgPackage() function
Anyhow, I hope this helps,