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smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
MIT License
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Pep on peptides first #2373

Closed trishorts closed 2 weeks ago

trishorts commented 3 weeks ago

We have been training our binary decision tree on psms rather than peptides. PSMs for the same peptide are not independent measurements. Therefore, they are not a good choice for ML training applications. This PR uses peptides instead and then applies that model to the PSMs.

Also, there are some efficiency and orangizational improvements.

codecov[bot] commented 2 weeks ago

Codecov Report

Attention: Patch coverage is 95.16129% with 6 lines in your changes missing coverage. Please review.

Project coverage is 92.85%. Comparing base (a025ca0) to head (a1095fd).

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2373/graphs/tree.svg?width=650&height=150&src=pr&token=m0HXyK8tFy&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc)](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2373?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) ```diff @@ Coverage Diff @@ ## master #2373 +/- ## ========================================== + Coverage 92.81% 92.85% +0.04% ========================================== Files 137 137 Lines 21188 21242 +54 Branches 2929 2931 +2 ========================================== + Hits 19666 19725 +59 + Misses 1042 1040 -2 + Partials 480 477 -3 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2373?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | Coverage Δ | | |---|---|---| | [...pheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2373?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FFdrAnalysis%2FFdrAnalysisEngine.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0ZkckFuYWx5c2lzL0ZkckFuYWx5c2lzRW5naW5lLmNz) | `96.52% <100.00%> (+0.02%)` | :arrow_up: | | [...eus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2373?src=pr&el=tree&filepath=MetaMorpheus%2FTaskLayer%2FSearchTask%2FPostSearchAnalysisTask.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9TZWFyY2hUYXNrL1Bvc3RTZWFyY2hBbmFseXNpc1Rhc2suY3M=) | `93.26% <100.00%> (ø)` | | | [...EngineLayer/FdrAnalysis/PEPValueAnalysisGeneric.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2373?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FFdrAnalysis%2FPEPValueAnalysisGeneric.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0ZkckFuYWx5c2lzL1BFUFZhbHVlQW5hbHlzaXNHZW5lcmljLmNz) | `95.71% <93.54%> (-0.39%)` | :arrow_down: | ... and [2 files with indirect coverage changes](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2373/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc)