Deprecation of functions

[lmsimp]

@lgatto What is your opinion on deprecating addGoAnnotation, setAnnotationParams and makeGoSet and functions that depend on Biomart? I don't personally use these and know they are not used by collaborators and those in the lab. I think you suggested this as a place to start last year when it came to cleaning things up.

Another candidate for deprecation is phenoDisco and related functions. I've also thought about the transfer learning algorithm but perhaps would like to keep the framework alive even if we don't provide a framework to explicitly create a GO set, my experience is if it is used users create and provide their own auxiliary data.

[lgatto]

My preference of the the biomaRt functions, as these create a substantial maintenance burden. Your other suggestions don't, so we can keep them, at least for now.

[lgatto]

• The first step would simply be to call .Deprecated() at the top of each of these.
• I'm not sure if we then would want to completely remove them, or move them somewhere so that somebody could still source that script and use them, but at their own risk, and without providing any support. Probably the former.