A feature based random forest model to priotize neoepitopes. This repository is bulid for tool usage. Look at all scripts made for the paper at: https://github.com/SRHgroup/IMPROVE_paper (will be made public upon acceptance)
- Feature_calculations.py
- Preidct_immunogenicity.py
Feature_calculations.py calculates all features used for the simple model besides:
NetMHCExp and Expression: These two features can be obtained by this tool:
Forginess score: Can be obtained by https://github.com/andrewrech/antigen.garnish
Save all programs to a folder
https://github.com/GfellerLab/PRIME
https://github.com/GfellerLab/MixMHCpred
https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/
https://services.healthtech.dtu.dk/services/NetMHCstabpan-1.0/
https://github.com/SRHgroup/self_similarity
Save all tools to a folder used for the feature calculation "--ProgramDir"
PrioScore: Priority score from Mupexi: https://services.healthtech.dtu.dk/services/MuPeXI-1.1/
CelPrev: Obtained from PyClone: https://github.com/Roth-Lab/pyclone
CYT: Geometric mean of GZMA and PRF1
MCPmean: Mean score of the 10 cell populations estimated from MCP-Counter
You can predit with three diffrent versions:
- Simple: All features from simple model and addition of NetMHCExp, Expression and Foreginess score
- TME excluded: All features from simple model with addition of priority score and cellular prevelance
- TME included: All features from TME excluded including RNA feature: CYT (geometirc mean of GZMA and PRF1) and MCP-mean gained from MCP-counter.
python3 bin/feature_calculations.py --file data/test_file_for_feature_calculation_small.tsv --dataset "testing" --ProgramDir "/Users/annieborch/Documents/programs/" --outfile "data/calculated_features_test.tsv" --TmpDir "/Users/annieborch/Documents/programs/"
python3 bin/Predict_immunogenicity.py --file data/calculated_features_test.tsv --model TME_excluded --outfile "output_prediction_tme_excluded.tsv"
python3 bin/Predict_immunogenicity.py --file data/calculated_features_test.tsv --model TME_included --outfile "output_prediction_tme_included.tsv"
python3 bin/Predict_immunogenicity.py --file data/calculated_features_test.tsv --model Simple --outfile "output_prediction_simple.tsv"