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masato-ogishi / Repitope

Epitope immunogenicity prediction through in silico TCR-peptide contact potential profiling.
MIT License
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Questions about the parameter fragDepth #4

Closed songofbin closed 5 years ago

songofbin commented 5 years ago

Hi Masato,

I have questions about the parameter fragDepth.

1, I think function CPP_FragmentLibrary doesn't have a parameter "maxFragDepth", it should be "fragDepth".

2, I was wondering why fragDepth was setting differently when building fragLibDT and Epitope prioritization?

fragLibDT <- CPP_FragmentLibrary(TCRSet_Public, fragLenSet=3:11, maxFragDepth=100000, seedSet=1:5)

res_MHCI <- EpitopePrioritization( featureDF=featureDF_MHCI[Peptide%in%MHCI_Human$Peptide,], metadataDF=MHCI_Human[,.(Peptide,Immunogenicity)], peptideSet=peptideSet_of_interest, fragLib=fragLibDT, aaIndexIDSet="all", fragLenSet=3:8, fragDepth=10000, fragLibType="Weighted", featureSet=MHCI_Human_MinimumFeatureSet, seedSet=1:5, coreN=parallel::detectCores(logical=F), outDir="./Output" ## Intermediate and final output files will be stored under this directory )

masato-ogishi commented 5 years ago

I originally tested the framework with different fragDepth (100, 1000, 10000, 100000). The parameter maxFragDepth is basically the maximum number of fragments retained in the Fragment Library. By setting this parameter to 100000, I reused the library for subsequent analysis. In other words, maxFragDepth should always be >=fragDepth. I thought fragDepth=10000 was fine, and did subsequent analyses. So you can just set maxFragDepth=10000.