Mann whitney test

[JanniRoebbecke]

Description

• Adds new method Mann-Whitney Test for differential Expression testing
• the new Method exists in two variants one with the operation differential_expression and one the method Peptide analysis
• the first takes any protein dataframe and returns a dictionary in the same format as the other methods in differential differential_expression. The output may be used to generate a volcano plot
• the second takes a 'ptm_df' from the a 'PTMs per Sample' Step and returns it's output in wide format

Changes

• the methods were implemented
• the Forms and Step Classes have been defined
• tests were implemented

Testing

• tests have been implemented
• import protein, meta and evidence file
• preprocess
• add Mann-Whitney Test with operation differential_expression and calculate
• add 'PTMs per Sample' Step and Mann-Whitney Test with operation Peptide analysis after that and calculate

PR checklist

Development

• [ ] If necessary, I have updated the documentation (README, docstrings, etc.)
• [ ] If necessary, I have created / updated tests.

Mergeability

• [ ] main-branch has been merged into local branch to resolve conflicts
• [ ] The tests and linter have passed AFTER local merge
• [ ] The code has been formatted with black

Code review

• [ ] I have self-reviewed my code.
• [ ] At least one other developer reviewed and approved the changes

[github-actions[bot]]

Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
protzilla
run.py
run_helper.py
runner.py
protzilla/data_analysis
differential_expression_anova.py
differential_expression_linear_model.py
differential_expression_mann_whitney.py					95, 263
differential_expression_t_test.py
protein_graphs.py
ptm_analysis.py					115-116, 134-136
protzilla/data_integration
di_plots.py
enrichment_analysis_gsea.py
protzilla/data_preprocessing
outlier_detection.py
transformation.py
protzilla/importing
ms_data_import.py					122, 276
peptide_import.py
protzilla/methods
data_analysis.py					164, 230-233, 761, 780
data_preprocessing.py
importing.py					142
protzilla/utilities
transform_dfs.py
utilities.py
ui/main
settings.py
ui/runs
fields.py
views.py
views_helper.py
ui/runs/forms
data_analysis.py					42-43, 307-311, 341, 360-364, 1039-1047, 1092, 1108, 1114
Project Total

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