dandelion.preprocessing.quantify_mutations

dandelion.preprocessing.quantify_mutations(self, split_locus=False, region_definition=None, mutation_definition=None, frequency=True, combine=True)

Runs basic mutation load analysis implemented in shazam.

Parameters

• self (Dandelion) – Dandelion object

• split_locus (bool) – whether to return the results for heavy chain and light chain separately. Default is False.

• region_definition (str, optional) – passed to shazam’s observedMutations.

• mutation_definition (str, optional) – passed to shazam’s observedMutations.

• frequency – whether to return the results a frequency or counts. Default is True (frequency).

• combine – whether to return the results for replacement and silent mutations separately (False). Default is True (sum).

Returns

Return type

Dandelion object with updated .metadata slot.