Update q-value calculation method #128
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When using the Pyteomics
qvaluesfunction, the formula argument was not set, assuming the default would be the regular first formula. However, asremove_decoyis set toFalse, the second, overly conservative, formula was used.See pyteomics.auxiliary.target_decoy.qvalues.
Additionally, the "+1" correction is now added:
The end-result is a more standard q-value calculation that is not as overly conservative. For instance, on the example file
example_files/msms.txt: