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fix: multiply standard error by zscore in calculate_confidence_interval #268

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merged 2 commits into from
Nov 22, 2023
Merged

fix: multiply standard error by zscore in calculate_confidence_interval #268

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2eee6ca
fix: multiply standard error by zscore in `calculate_confidence_inter…
ireneisdoomed Nov 21, 2023
4635b99
chore: remove reference to confidence intervals
ireneisdoomed Nov 22, 2023
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15 changes: 10 additions & 5 deletions src/otg/common/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -86,9 +86,9 @@ def calculate_confidence_interval(
+---------------+---------------+----+--------------+---------------------------+---------------------------+
|pvalue_mantissa|pvalue_exponent|beta|standard_error|betaConfidenceIntervalLower|betaConfidenceIntervalUpper|
+---------------+---------------+----+--------------+---------------------------+---------------------------+
| 2.5| -10| 0.5| 0.2| 0.3| 0.7|
| 3.0| -5| 1.0| null| 0.7603910153486024| 1.2396089846513976|
| 1.5| -8|-0.2| 0.1| -0.30000000000000004| -0.1|
| 2.5| -10| 0.5| 0.2| 0.10799999999999998| 0.892|
| 3.0| -5| 1.0| null| 0.5303663900832607| 1.4696336099167393|
| 1.5| -8|-0.2| 0.1| -0.396| -0.00400000000000...|
+---------------+---------------+----+--------------+---------------------------+---------------------------+
<BLANKLINE>
"""
Expand All @@ -104,8 +104,13 @@ def calculate_confidence_interval(
).otherwise(standard_error)

# Calculate upper and lower confidence interval:
ci_lower = (beta - standard_error).alias("betaConfidenceIntervalLower")
ci_upper = (beta + standard_error).alias("betaConfidenceIntervalUpper")
z_score_095 = 1.96
ci_lower = (beta - z_score_095 * standard_error).alias(
"betaConfidenceIntervalLower"
)
ci_upper = (beta + z_score_095 * standard_error).alias(
"betaConfidenceIntervalUpper"
)

return (ci_lower, ci_upper)

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5 changes: 0 additions & 5 deletions tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -410,11 +410,6 @@ def mock_summary_statistics_data(spark: SparkSession) -> DataFrame:
# Making sure p-values are below 1:
).build()

# Because some of the columns are not strictly speaking required, they are dropped now:
data_spec = data_spec.drop(
"betaConfidenceIntervalLower", "betaConfidenceIntervalUpper"
)

return data_spec


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