scvi.data.reads_to_fragments

scvi.data.reads_to_fragments#

scvi.data.reads_to_fragments(adata, read_layer=None, fragment_layer='fragments')[source]#

Convert scATAC-seq read counts to appoximate fragment counts.

Parameters:

  • adata (AnnData) – AnnData object that contains read counts.

  • read_layer (str | None (default: None)) – Key in`.layer` that the read counts are stored in.

  • fragment_layer (str (default: 'fragments')) – Key in`.layer` that the fragment counts will be stored in.

Return type:

None

Returns:

Adds layer with fragment counts in .layers[fragment_layer].

Contents