smftools.preprocessing.binarize

Functions

binarize_adata(adata[, source, ...])

Binarize a dense matrix and preserve NaNs.

smftools.preprocessing.binarize.binarize_adata(adata, source='X', target_layer='binary', threshold=0.8)

Binarize a dense matrix and preserve NaNs.

Parameters:

• adata (AnnData) -- AnnData object with input matrix or layer.

• source (str (default: 'X')) -- "X" to use the main matrix or a layer name.

• target_layer (str (default: 'binary')) -- Layer name to store the binarized values.

• threshold (float (default: 0.8)) -- Threshold above which values are set to 1.

Return type:

None