carmapy

Python implementation of the CARMA R Package¹ for fine-mapping (work in progress).

Installation:

• Tested with Python 3.9.6 and cython 0.29.36

pip install -r requirements.txt
python setup.py build_ext --inplace
pip install .

Sample data to test CARMA available in /tests or from: https://zenodo.org/record/7772462 (file to download: Sample_data.tar.gz)

To Test:

1. Make changes to carmapy/carma_normal_fixed_sigma.py
2. Update file paths:
   • Line 2 sys.path.append() of tests/carma_test.py and tests/carma_py_functions_test.ipynb
   • Update file paths to load sumstats and ld
3. Run python ./tests/carma_test.py to test whole fine-mapping process or test individual functions in tests/carma_py_functions_test.ipynb

Notes:

• tests/carma_py_functions_test.ipynb function outputs need to equal to those in tests/carma_r_functions_test.ipynb

• tests/carma_cython_test.ipynb function outputs need to equal to those in tests/carma_rcpp_test.ipynb

Reference:

1. Yang, Z., Wang, C., Liu, L. et al. CARMA is a new Bayesian model for fine-mapping in genome-wide association meta-analyses. Nat Genet 55, 1057–1065 (2023). https://doi.org/10.1038/s41588-023-01392-0