scirpy.get.airr

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scirpy.get.airr#

scirpy.get.airr(adata, airr_variable, chain=('VJ_1', 'VDJ_1', 'VJ_2', 'VDJ_2'), *, airr_mod='airr', airr_key='airr', chain_idx_key='chain_indices')#

Retrieve AIRR variables for each cell, given a specific chain.

Parameters:

  • adata (Union[AnnData, MuData, DataHandler]) – AnnData or MuData object that contains AIRR information.

  • airr_variable (Union[str, Sequence[str]]) – One or multiple columns from the AIRR Rearrangment schema (see adata.var). If multiple values are specified, a dataframe will be returned.

  • chain (Union[Literal['VJ_1', 'VJ_2', 'VDJ_1', 'VDJ_2'], Sequence[Literal['VJ_1', 'VJ_2', 'VDJ_1', 'VDJ_2']]] (default: ('VJ_1', 'VDJ_1', 'VJ_2', 'VDJ_2'))) – choose the recptor arm (VJ/VDJ) and if you want to retrieve the primary or secondary chain. If multiple chains are specified, a adataframe will be returned

  • airr_mod (str (default: 'airr')) – Name of the modality with AIRR information is stored in the MuData object. if an AnnData object is passed to the function, this parameter is ignored.

  • airr_key (str (default: 'airr')) – Key under which the AIRR information is stored in adata.obsm as an awkward array.

  • chain_idx_key (str (default: 'chain_indices')) – Key under which the chain indices are stored in adata.obsm. If chain indices are not present, index_chains() is run with default parameters.

Return type:

Union[DataFrame, Series]

Returns:

A Series or DataFrame aligned to adata.obs. Contains missing values in places where a cell does not have the requested chain.

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