scmagnify.import_basalGRN

scmagnify.import_basalGRN#

scmagnify.import_basalGRN(basal_grn, adata, gene_selected=None, layer='counts', verbose=True)#

Import a provided basal GRN and align it to the given AnnData.

Parameters:

  • basal_grn (DataFrame) – DataFrame with columns [‘TF’, ‘Target’] (and optional ‘Score’).

  • adata (AnnData) – Annotated data object.

  • gene_selected (Optional[Index] (default: None)) – Genes to include; if None, uses intersection with basal GRN genes.

  • layer (str (default: 'counts')) – Layer in layers. If None, defaults to X.

  • verbose (bool (default: True)) – Whether to print summary statistics.

Return type:

tuple[AnnData, DataFrame]

Returns:

-adata_filtered (AnnData)

Filtered and normalized annotated data matrix.

-basal_grn (ndarray)

Binary prior network matrix aligned to (regulators x targets).

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