enable pep prefilter if available

smith-chem-wisc / FlashLFQ

Ultra-fast label-free quantification algorithm for mass-spectrometry proteomics

GNU Lesser General Public License v3.0

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enable pep prefilter if available #117

Open trishorts opened 2 years ago

trishorts commented 2 years ago

I may close this PR b/c it only effects the standalone version.

In MetaMorpheus, we are slowly moving on from q-value filter and relying more and more on PEP. This PR, tells FlashLFQ to prefilter on PEP and PEP Q-value if those parameters are specified. If they are not, the default reverts to q-value and q-value notch.