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muon.atac.pp.tfidf

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muon.atac.pp.tfidf#

muon.atac.pp.tfidf(data: AnnData | MuData, log_tf: bool = True, log_idf: bool = True, log_tfidf: bool = False, scale_factor: int | float = 10000.0, inplace: bool = True, copy: bool = False, from_layer: str | None = None, to_layer: str | None = None)#

Transform peak counts with TF-IDF (Term Frequency - Inverse Document Frequency).

TF: peak counts are normalised by total number of counts per cell DF: total number of counts for each peak IDF: number of cells divided by DF

By default, log(TF) * log(IDF) is returned.

Parameters:

  • data – AnnData object with peak counts or multimodal MuData object with ‘atac’ modality.

  • log_idf – Log-transform IDF term (True by default).

  • log_tf – Log-transform TF term (True by default).

  • log_tfidf – Log-transform TF*IDF term (False by default). Can only be used when log_tf and log_idf are False.

  • scale_factor – Scale factor to multiply the TF-IDF matrix by (1e4 by default).

  • inplace – If to modify counts in the AnnData object (True by default).

  • copy – If to return a copy of the AnnData object or the ‘atac’ modality (False by default). Not compatible with inplace=False.

  • from_layer – Layer to use counts (AnnData.layers[from_layer]) instead of AnnData.X used by default.

  • to_layer – Layer to save transformed counts to (AnnData.layers[to_layer]) instead of AnnData.X used by default. Not compatible with inplace=False.

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