search

thomasp85 / MSGFgui

A gui overlay and extension for MSGFplus
10 stars 6 forks source link

Add option to use results from first search to train MS-GF+ scoring parameters #31

Open jgmeyerucsd opened 9 years ago

jgmeyerucsd commented 9 years ago

My personal favorite feature of MS-GF+ is that the program allows one to use the results from a search to re-train the scoring parameters for your specific type of peptides. This feature is especially useful for those of us who are running non-standard proteomics experiments, e.g. modifications, new digestions, new fragmentation parameters. It would be cool if your GUI had a checkbox that automatically used your first results as a training set and re-searched the data with the new .params files. I'll look at your code and see if I think I can do this myself.

thomasp85 commented 9 years ago

I'm not in any way opposed to this but at the moment my focus is elsewhere. It should be relatively straightforward to add the possibility to MSGFplus, while adding it to the GUI will require quite a lot more...

jgmeyerucsd commented 9 years ago

I starting editing your files to add the functionality to the MSGFplus package, but it wont let me fork your package. Is that something you set or is there an error on my end?

Best, Jesse

From: Thomas Lin Pedersen [notifications@github.com] Sent: Wednesday, July 22, 2015 1:09 AM To: thomasp85/MSGFgui Cc: Jesse G Meyer Subject: Re: [MSGFgui] Add option to use results from first search to train MS-GF+ scoring parameters (#31)

I'm not in any way opposed to this but at the moment my focus is elsewhere. It should be relatively straightforward to add the possibility to MSGFplus, while adding it to the GUI will require quite a lot more...

— Reply to this email directly or view it on GitHubhttps://github.com/thomasp85/MSGFgui/issues/31#issuecomment-123610181.

thomasp85 commented 9 years ago

Sorry for being slow on the responce - I've been suffering a concussion...

There should be no restrictions on forking - do you get an error?