How does "matched_intensity_df" from ModelManager.train_ms2_model (pretrain_model.py) look like?

MannLabs / alphapeptdeep

Deep learning framework for proteomics

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How does "matched_intensity_df" from ModelManager.train_ms2_model (pretrain_model.py) look like? #113

Closed HojunYou closed 10 months ago

HojunYou commented 10 months ago

Hello, thanks for such a useful package!

I've been trying to fine-tune ms2_model from ModelManager object, but I'm having hard time figuring out how "matched_intensity_df" data frame looks like. Could you describe the structure of the data frame? or provide a sample. Thank you so much!

jalew188 commented 10 months ago

Please check https://github.com/MannLabs/alphapeptdeep/blob/main/nbdev_nbs/psm_frag_reader/psmlabel_reader.ipynb and https://github.com/MannLabs/alphapeptdeep/blob/main/nbdev_nbs/psm_frag_reader/maxquant_frag_reader.ipynb