alphapepttools.pp.impute_median

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alphapepttools.pp.impute_median#

alphapepttools.pp.impute_median(adata, group_column=None, layer=None, *, inplace=True)#

Impute missing values using median imputation

Replace missing (NaN) values in the data matrix with the median of non-missing values for each feature. Can perform global imputation using all samples or group-wise imputation using subsets of samples defined by a categorical variable.

Parameters:

  • adata (AnnData) – AnnData object

  • layer (str | None (default: None)) – Layer to use for imputation

  • group_column (str | None (default: None)) – Column name in adata.obs defining groups for group-wise imputation. If None (default), computes median across all samples. Defines a group column that is used to subset the samples that should be used for imputation. If specified, computes median separately for each group and imputes missing values using the group-specific median. If group_column contains NaNs, the respective observations are ignored.

  • inplace (bool (default: True)) – If True (default), modifies adata inplace and returns None. If False, returns a modified copy of adata.

  • copy –

    Deprecated since version 0.5.0: Use inplace instead. copy will be removed in version 0.6.0.

Return type:

AnnData | None

Returns:

AnnData object with imputed values in layer. If inplace=True modifies the anndata object at layer inplace and returns None. If inplace=False, returns a modified copy.

Raises:

  • Warning – If group_column contains NaNs

  • Warning – If a feature contains only NaNs

Notes

Features that are fully missing will not be imputed. Appropriate filtering of features with at.pp.filter_data_completeness() is critical.

Example

Impute the values in the .X matrix

adata = at.pp.impute_median(adata)
assert np.sum(np.isnan(adata.X)) == 0

Impute data in a specific layer

adata = at.pp.impute_median(adata, layer="layer2")
assert np.sum(np.isnan(adata.layers["layer2"])) == 0

Impute groupwise based on a categorical column:

adata = at.pp.impute_median(adata, group_column="cell_type")
# Imputes group-wise medians
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