dandelion.external.immcantation.base.shazam.quantify_mutations

dandelion.external.immcantation.base.shazam.quantify_mutations(data, split_locus=False, sequence_column=None, germline_column=None, region_definition=None, mutation_definition=None, frequency=False, combine=True, **kwargs)

Run basic mutation load analysis.

Implemented in shazam https://shazam.readthedocs.io/en/stable/vignettes/Mutation-Vignette.

Parameters:

• data (Dandelion | str) – Dandelion object, file path to AIRR file.

• split_locus (bool, optional) – whether to return the results for heavy chain and light chain separately.

• sequence_column (str | None, optional) – passed to shazam’s observedMutations. https://shazam.readthedocs.io/en/stable/topics/observedMutations

• germline_column (str | None, optional) – passed to shazam’s observedMutations. https://shazam.readthedocs.io/en/stable/topics/observedMutations

• region_definition (str | None, optional) – passed to shazam’s observedMutations. https://shazam.readthedocs.io/en/stable/topics/IMGT_SCHEMES/

• mutation_definition (str | None, optional) – passed to shazam’s observedMutations. https://shazam.readthedocs.io/en/stable/topics/MUTATION_SCHEMES/

• frequency (bool, optional) – whether to return the results a frequency or counts.

• combine (bool, optional) – whether to return the results for replacement and silent mutations separately.

• **kwargs – passed to shazam::observedMutations.

Returns:

pandas DataFrame holding mutation information.

Return type:

DataFrame