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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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[WIP] filter psms for flashlfq only by qvalue and qvalue notch #2259

Open trishorts opened 1 year ago

trishorts commented 1 year ago

this code was changed in a prior commit https://github.com/smith-chem-wisc/MetaMorpheus/pull/2161 Files with values for PEP were filtered by PEP. But when assigning them to ProteinGroups, the filter was for qvalue and qvalue notch. Thus there was incosistency that produced UNDEFINED protein groups for some peptides. This messed up protein quantification.

codecov[bot] commented 1 year ago

Codecov Report

Merging #2259 (e5158ee) into master (8d84c84) will decrease coverage by 0.01%. The diff coverage is 100.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #2259      +/-   ##
==========================================
- Coverage   91.44%   91.43%   -0.01%     
==========================================
  Files         134      134              
  Lines       20167    20158       -9     
  Branches     2809     2807       -2     
==========================================
- Hits        18441    18432       -9     
  Misses       1237     1237              
  Partials      489      489
Impacted Files Coverage Δ
TaskLayer/SearchTask/PostSearchAnalysisTask.cs 92.50% <100.00%> (-0.06%) :arrow_down: