rcParams and configuration

FLiPPR exposes a small configuration dictionary, rcParams, defined in src/flippr/parameters.py.

Common configuration keys include:

  • ion.missing_intensity_thresh : threshold for missing ion intensities

  • ion.aon_impute_loc, ion.aon_impute_scale : parameters for AON imputation

  • trp_protein.intensity_value : which TrP protein intensity column to use (e.g. “MaxLFQ Intensity”)

  • significance thresholds for proteins and TrP-derived normalization: - trp_protein.fc_sig_tresh, trp_protein.pval_sig_tresh - protein.fc_sig_sig_thresh, protein.pval_sig_thresh, protein.adj_pval_sig_thresh

Modify rcParams before running a study, for example:

from flippr.parameters import rcParams
rcParams["ion.missing_intensity_thresh"] = 2

Refer to src/flippr/parameters.py for the full list of keys and defaults.