.utils

Note

Only the functions listed below are part of the public API and officially supported. All other functions in proteopy.utils are internal helpers and may change without notice.

Data Validation

proteopy.utils.is_proteodata	Check whether the AnnData object stores peptide- or protein-level proteomics data.
proteopy.utils.check_proteodata	Validate that adata satisfies ProteoPy assumptions, raising on failure.

Array Utilities

proteopy.utils.is_log_transformed

Heuristic detector for log-transformed matrices.

Proteoform Group Simulation

Simulate proteoform groups to evaluate how well a proteoform inference method recovers them in a dataset, optionally with simulated batch effects to evaluate batch-aware inference.

proteopy.utils.proteoform_group_simulator	Iterate over peptide-level datasets with planted proteoform groups.
proteopy.utils.proteoform_simulation_metrics	Measure how well planted proteoform groups were recovered.
proteopy.utils.apply_peptide_batch_effects	Simulate peptide-specific batch effects in peptide-level data.

Plotting

proteopy.utils.volcano_plot

Volcano plot renderer (framework-agnostic).