Reworking PEP to prevent cross-contamination #2394
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trishorts
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| /// e.g., partition 1 = [0, 4, 8...], partition 2 = [1, 5, 9...], etc. | ||
| /// </summary> | ||
| /// <returns>A list containing numGroups partitions (lists of ints) </returns> | ||
| static List<List<int>> DivideListIntoGroups(List<int> list, int numGroups) |
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there was a previously less complicated method here. did it not function correctly?
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previously, the method took sequential chunks from each list. e.g., [1,2,3,4,5,6,7,8] would return [[1, 2], [3, 4], [5, 6], [7, 8]].
This function would return [[1, 5], [2, 6], [3, 7], [4, 8]].
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MetaMorpheus/EngineLayer/FdrAnalysis/PEPValueAnalysisGeneric.cs
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This PR changes how the PEP Engine works in order to prevent contamination during cross validation. It also changes how decoys are generated.
PEP Changes
In PEP, all PSMs that correspond to the same sequence are grouped together. The PeptideMatchGroup class enables this, acting as a collection of PSMs that all correspond to the same base sequence.
Then, the PEP engine splits the PeptideMatchGroups into 4 partitions. All PSMs in one partition have their PEPs calculated using a model trained on data from the other three partitions.
Decoy changes
When databases are loaded in MetaMorpheusTask, there is a new step that removes decoy peptides that are identical to target peptides. This is done by modifying the base sequence of each decoy protein to scramble and sequences that are identical to a target peptide.