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fix(imputation): add missing CpGs from source in impute_from_standard #187

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Merged
marcbal77 merged 1 commit into from
Dec 5, 2025
Merged

fix(imputation): add missing CpGs from source in impute_from_standard #187

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1 change: 1 addition & 0 deletions biolearn/imputation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ def impute_from_standard(dnam, cpg_source, cpgs_to_impute=None):
pd.DataFrame: DataFrame with missing values filled.
"""
if cpgs_to_impute:
dnam = dnam.reindex(dnam.index.union(cpgs_to_impute))
impute_rows = dnam.loc[cpgs_to_impute]
impute_rows = impute_rows.apply(lambda col: col.fillna(cpg_source))
df_filled = dnam.combine_first(impute_rows)
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9 changes: 9 additions & 0 deletions biolearn/test/test_imputation.py
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Expand Up @@ -38,6 +38,15 @@ def test_impute_from_standard():
assert df_filled.loc["cpg2", "Sample1"] == 2.5


def test_impute_from_standard_adds_missing_cpgs():
cpgs_with_missing = ["cpg1", "cpg5"]
df_filled = impute_from_standard(
df_test, cpg_averages_test, cpgs_to_impute=cpgs_with_missing
)
assert "cpg5" in df_filled.index
assert df_filled.loc["cpg5", "Sample1"] == 5.5


def test_impute_from_standard_specific_cpgs():
specific_cpgs = ["cpg1", "cpg3"]
df_filled = impute_from_standard(
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