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Add min_peaks config option #264

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wsnoble opened this issue Nov 10, 2023 · 1 comment
Open

Add min_peaks config option #264

wsnoble opened this issue Nov 10, 2023 · 1 comment
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enhancement New feature or request good first issue Good for newcomers

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@wsnoble
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wsnoble commented Nov 10, 2023

Casanovo should have a configuration option that specifies the minimum number of peaks that are required to be in a spectrum before it will make a prediction. Currently, Casanovo will happily make a prediction (sometimes with a high score) even if the spectrum has only a handful of peaks. The default value for the analogous parameter in Tide is 20 and in Comet is 10. For de novo, I think we should use a default of 20. This is the minimum in the 9-species benchmark.

Note that, ideally, Casanovo would track and then report something like "Info: XXX spectra skipped because they have fewer than XX peaks."

@wsnoble wsnoble added the good first issue Good for newcomers label Nov 10, 2023
@bittremieux bittremieux added the enhancement New feature or request label Nov 13, 2023
@bittremieux
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Postponed until functionality from DepthCharge v0.3 has been integrated, which will make this very easy to implement.

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Labels
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