Update makeGoSet doc - Githubissues

lgatto / pRoloc

A unifying bioinformatics framework for organelle proteomics

http://lgatto.github.io/pRoloc/

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Update makeGoSet doc #57

Open lmsimp opened 9 years ago

lmsimp commented 9 years ago

Add a note about GO hierarchy
Add a note/link about filterBinMSnSet
In paper: @lmsimp to complete
update TL vignette and load TL params rda file. Then remove then from andy2011.

Maybe also add a note in the vignette.

lgatto commented 8 years ago

@lmsimp - reminder about this issue: has these been done?

lgatto commented 1 month ago

There are major differences in the makeGoSet() example, that now returns only two GO terms. Not sure what happens. It might not be a problem, and just be the result of using old parameters to retrieve the terms, but I had to fix some examples. I am wondering if this GO functionality is still relevant and whether it could be deprecated. @lmsimp what do you think?

lmsimp commented 1 month ago

I haven't used this functionality in a while now. Initial thoughts are yes... I will take a look and confirm. If we were to remove makeGoSet would this allow removal of biomaRt from dependencies?

lgatto commented 1 month ago

The whole vignette annotation stuff gets dropped (vignette 4), and part of the transfer learning (vignette 5). It would be quite radical.