dandelion.preprocessing.quantify_mutations¶
-
dandelion.preprocessing.
quantify_mutations
(self, split_locus=False, sequence_column=None, germline_column=None, region_definition=None, mutation_definition=None, frequency=True, combine=True)[source]¶ Runs basic mutation load analysis implemented in shazam.
- Parameters
self (Dandelion, str, PathLike) – Dandelion object, file path to AIRR file.
split_locus (bool) – whether to return the results for heavy chain and light chain separately. Default is False.
sequence_column (str, optional) – passed to shazam’s observedMutations. https://shazam.readthedocs.io/en/stable/topics/observedMutations
germline_column (str, optional) – passed to shazam’s observedMutations. https://shazam.readthedocs.io/en/stable/topics/observedMutations
region_definition (str, optional) – passed to shazam’s observedMutations. https://shazam.readthedocs.io/en/stable/topics/IMGT_SCHEMES/
mutation_definition (str, optional) – passed to shazam’s observedMutations. https://shazam.readthedocs.io/en/stable/topics/MUTATION_SCHEMES/
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.