Inconsistency in Distance Calculation and Occurrences in expected_interactions and obs_exp_matrix

[mhjiang97]

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Description

There is an inconsistency in the way distances and occurrences are handled in the expected_interactions obs_exp_matrix functions in utilities.py. Specifically, the obs_exp_matrix function divides the distance by 2, while the expected_interactions function does not account for the symmetry of the Hi-C matrix in its occurrences calculation.

Expected Behavior

The distance calculation and occurrences should be consistent across both functions. The occurrences should account for the symmetry of the Hi-C matrix, except for the main diagonal.

Actual Behavior

• The obs_exp_matrix function divides the distance by 2.
  Line 578 in utilities.py:

  distance = np.ceil(np.absolute(row - col) / 2).astype(np.int32)

• The expected_interactions function does not account for the symmetry of the Hi-C matrix in its occurrences calculation.
  Line 364 in utilities.py:

  occurrences = np.arange(pSubmatrix.shape[0] + 1, 1, -1)

I'm concerned about this implementation but unsure if my concerns are valid. I look forward to your response. Thank you!