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openvax / mhcflurry

Peptide-MHC I binding affinity prediction
http://openvax.github.io/mhcflurry/
Apache License 2.0
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Does training data contain mass-spec data? #121

Closed weipenegHU closed 6 years ago

weipenegHU commented 6 years ago

Hi Donnell, I am curious about if the latest version of MHCflurry is trained on both mass-spec data and binding data set

timodonnell commented 6 years ago

The default predictor for the current release is trained on only affinity measurements (no mass spec) but the model selection step incorporates mass spec. We also release experimental predictors whose training data directly includes mass spec though, they just aren't the default. If you want to use predictors trained directly on mass spec you can run:

$ mhcflurry-downloads fetch models_class1_trained_with_mass_spec

and then to make them used by default:

export MHCFLURRY_DEFAULT_CLASS1_MODELS="$(mhcflurry-downloads path models_class1_trained_with_mass_spec)/models"

Let me know if you have any questions. Leaving this issue open as a reminder for us to add the above to the documentation sometime soon.

weipenegHU commented 6 years ago

Thanks for your information