API Reference

This page summarizes the public API used by typical FLiPPR workflows.

Study

Class: Study

  • Constructor: Study(lip: str | Path, trp: Optional[str | Path] = None, method: str = “dda”)

  • Properties: samples (dict)

  • Methods: add_process(pid, lip_ctrl, lip_test, n_rep, trp_ctrl=None, trp_test=None, trp_n_rep=None), run()

Process & Result

Process and Result are types used internally and returned by Study.run().

  • Result exposes dataframes and summary tables: - ion : ion-level polars.DataFrame - peptide : peptide-level polars.DataFrame - modified_peptide : modified peptide-level polars.DataFrame - cut_site : cut-site-level polars.DataFrame - protein_summary : protein summary polars.DataFrame - name : human-readable process name

Combine helpers

The module-level helpers in combine.py are convenient for downstream aggregation:

  • combine_by(df: polars.DataFrame, by: str, fc: str) -> polars.DataFrame

  • summary_by(df: polars.DataFrame, by: str, fc: str, rcParams: dict) -> polars.DataFrame

Notes

Many functions under src/flippr use a leading underscore to indicate internal utilities. The public surface is primarily the Study class and the combine helpers.