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Refactor: remove deprecated _change_lfc_sign attribute of the DeseqStats class #47

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Merged
BorisMuzellec merged 2 commits into from
Jan 13, 2023
Merged

Refactor: remove deprecated _change_lfc_sign attribute of the DeseqStats class #47

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7589632
refactor: remove useless print statement
Jan 12, 2023
d20b27d
refactor: remove deprecated _change_lfc_sign attribute
Jan 12, 2023
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8 changes: 0 additions & 8 deletions pydeseq2/DeseqStats.py
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Original file line number Diff line number Diff line change
Expand Up @@ -185,13 +185,11 @@ def __init__(
)
self.LFCs.iloc[:, 0] += self.LFCs.iloc[:, self.contrast_idx]
self.LFCs.iloc[:, self.contrast_idx] *= -1
print(self.LFCs.columns[self.contrast_idx])
# Set a flag to indicate that LFCs are unshrunk
self.shrunk_LFCs = False
self.n_processes = get_num_processes(n_cpus)
self.batch_size = batch_size
self.joblib_verbosity = joblib_verbosity
self._change_lfc_sign = False

def summary(self):
"""Run the statistical analysis.
Expand Down Expand Up @@ -256,12 +254,6 @@ def run_wald_test(self):
.values
)

# If the contrast implies a different reference level than the one from the
# design matrix, change lfc signs. Do this *after* the means were computed
# (otherwise we would need)
if self._change_lfc_sign:
self.LFCs.iloc[:, self.contrast_idx] *= -1

# Set regularization factors.
if self.prior_disp_var is not None:
ridge_factor = np.diag(1 / self.prior_disp_var**2)
Expand Down