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Remove ellipsis.
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@ielis
ielis committed Sep 26, 2023
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13 changes: 7 additions & 6 deletions docs/tutorial.rst
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Expand Up @@ -63,12 +63,12 @@ For instance, we can partition the patients into two groups based on presence/ab
>>> from genophenocorr.constants import VariantEffect
>>> cohort_analysis = CohortAnalysis(cohort, 'NM_1234.5', hpo, include_unmeasured=False)
>>> frameshift = cohort_analysis.compare_by_variant_type(VariantEffect.FRAMESHIFT_VARIANT)
>>> pprint(frameshift) # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
With frameshift_variant ... Without frameshift_variant
Count Percent ... Count Percent p-value
HP:0001166 (Arachnodactyly) 4 30.77% ... 10 76.92% 0.04718
HP:0001250 (Seizure) 11 84.62% ... 9 69.23% 0.64472
HP:0001257 (Spasticity) 8 61.54% ... 9 69.23% 1.00000
>>> pprint(frameshift, width=120) # doctest: +NORMALIZE_WHITESPACE
With frameshift_variant Without frameshift_variant
Count Percent Count Percent p-value
HP:0001166 (Arachnodactyly) 4 30.77% 10 76.92% 0.04718
HP:0001250 (Seizure) 11 84.62% 9 69.23% 0.64472
HP:0001257 (Spasticity) 8 61.54% 9 69.23% 1.00000
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Expand All @@ -83,6 +83,7 @@ Or perform similar partitioning based on presence/absence of a *missense* varian
HP:0001166 (Arachnodactyly) 13 81.25% 1 10.00% 0.000781
HP:0001257 (Spasticity) 11 68.75% 6 60.00% 0.692449
HP:0001250 (Seizure) 12 75.00% 8 80.00% 1.000000
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The tables present the HPO terms that annotate the cohort members and report their counts and p values
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