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masato-ogishi / Repitope

Epitope immunogenicity prediction through in silico TCR-peptide contact potential profiling.
MIT License
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Task 120 failed / featureDFList_MHCI #3

Closed FabriceRenaud closed 5 years ago

FabriceRenaud commented 5 years ago

Hi Masato,

Thank you for providing your code!

I want to run your code with a small dataset of my own containing 459 unique peptides of variable length between 5 and 18 amino acids.

I create my own data.table(MHCI_Human) with the same colnames as yours. But I'm not using Epitope_Import() to create it.

When I run the Features function I got the following error right after I the "Peptide descriptor analysis" message.:

Error in { : task 120 failed - "Argument 'x' must be a matrix or a vector."

I believe the error come when peptideDescriptor.FragStat.Single() is called.

Being a beginner with those kind of code I'm struggling to identify what causes the error but I have two potential ideas: 1) I should create my MHCI_Human database by using Epitope_Import() to have the appropriate data structure? 2) Fragment size must be 8-11 or at least >=8mer ?

Do I make an obvious mistake here? Thanks in advance,

Fabrice

paulrbuckley commented 4 years ago

Having the same issue. Any chance you remember what the solution was?

cheers

P