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PyProphet / pyprophet

PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
http://www.openswath.org
BSD 3-Clause "New" or "Revised" License
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[ADD] ScoreFilter #83

Closed oliveralka closed 4 years ago

oliveralka commented 4 years ago

Add a score filter, which also supports possible score combinations for given analysis e.g. metabolomics.

I am not sure if that fits the pyprophet data structure as it is. There also seems to be an incompatibility with different scoring levels (seems to work only using ms1ms2).

@grosenberger Could you take a look and give me some pointers on how the integration could be improved. Afterwards, I will add some additional tests.

grosenberger commented 4 years ago

This looks very nice, thanks! Shouldn't this also work on the other scoring levels if the selected scores are present there too? Except if you use the metabolomics set of course.

oliveralka commented 4 years ago

It should. I think I used ms1 and ms2 scores for ms1 scoring, which of course does not work... I will test this locally and will add additional test for the scoring filter parameter later today to this PR.

oliveralka commented 4 years ago

Ok, it works with the different levels. I had the misconception, that the MS1 scores are always "varms1..." which is not the case if --level=ms1. This may lead to confusion in the future when this option is used with individual levels. Should this be specified somewhere - without cluttering the parameter help?

oliveralka commented 4 years ago

@grosenberger Could you give it another look and let me know if anything should be added?