Feature: utils.apply_peptide_batch_effects()

HISTORY.md

@@ -63,6 +63,10 @@ and this project adheres to
 - `proteoform_simulation_metrics()`: after running proteoform
   inference on a simulated dataset, returns one record of metrics
   plus the per-protein results table.
+- `apply_peptide_batch_effects()`: simulates peptide-specific batch effects
+  (`flavor="subset_shift"`) by shifting `n_peptides` peptides per
+  protein by `log2fc` in selected (`batches` as list) or randomly
+  drawn (`batches` as int) batches of `batch_key`.
 
 ### Fixed
 

docs/sphinx/source/api/utils.rst

@@ -30,14 +30,16 @@
 .. rubric:: Proteoform Group Simulation
 
 Simulate proteoform groups to evaluate how well a proteoform inference
-method recovers them in a dataset.
+method recovers them in a dataset, optionally with simulated batch
+effects to evaluate batch-aware inference.
 
 .. autosummary::
    :toctree: generated/
    :nosignatures:
 
    proteopy.utils.proteoform_group_simulator
    proteopy.utils.proteoform_simulation_metrics
+   proteopy.utils.apply_peptide_batch_effects
 
 .. rubric:: Plotting
 

proteopy/utils/__init__.py

@@ -8,3 +8,4 @@
     proteoform_group_simulator,
     proteoform_simulation_metrics,
 )
+from .batch_effect_simulation import apply_peptide_batch_effects