scButterfly.data_processing.RNA_data_preprocessing

scButterfly.data_processing.RNA_data_preprocessing(RNA_data, normalize_total=True, log1p=True, use_hvg=True, n_top_genes=3000, save_data=False, file_path=None, logging_path=None)

Preprocessing for RNA data, we choose normalization, log transformation and highly variable genes, using scanpy.

Parameters:

  • RNA_data (Anndata) – RNA anndata for processing.

  • normalize_total (bool) – choose use normalization or not, default True.

  • log1p (bool) – choose use log transformation or not, default True.

  • use_hvg (bool) – choose use highly variable genes or not, default True.

  • n_top_genes (int) – the count of highly variable genes, if not use highly variable, set use_hvg = False and n_top_genes = None, default 3000.

  • save_data (bool) – choose save the processed data or not, default False.

  • file_path (str) – the path for saving processed data, only used if save_data is True, default None.

  • logging_path (str) – the path for output process logging, if not save, set it None, default None.

Returns:

RNA_data_processed – RNA data with normalization, log transformation and highly variable genes selection preprocessed.

Return type:

Anndata