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skip seak association testing if all burdens are constant #142

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Oct 28, 2024
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skip seak association testing if all burdens are constant #142

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skip seak association testing if all burdens are constant
HolEv Oct 21, 2024
a325f7c
fixup! Format Python code with psf/black pull_request
Oct 21, 2024
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3 changes: 3 additions & 0 deletions deeprvat/deeprvat/associate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1152,6 +1152,9 @@ def regress_on_gene_scoretest(
logger.warning(f"Burden for gene {gene} is 0 for all samples; skipping")
return None

if np.unique(burdens).shape[0] == 1:
logger.warning(f"Burdens for gene {gene} are all constant; skipping")
return None
pv = model_score.pv_alt_model(burdens)

logger.info(f"p-value: {pv}")
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