scrnatools.tools.create_isoform_lookup_tables

scrnatools.tools.create_isoform_lookup_tables(adata: AnnData, t2enst_path: DataFrame, t2g_path: DataFrame) → Tuple[Dict[str, str], Dict[str, str], Dict[str, str]]

Creates the lookup tables for isoform data transcripts and genes.

Parameters:

• adata (AnnData) – The AnnData containing kallisto isoform data.

• t2enst_path (DataFrame) – Path to the transcript to ensembl transcript id mapping dataframe (from kallisto alignment).

• t2g_path (DataFrame) – Path to the transcript to gene mapping dataframe (from the kallisto reference used for alignment).

Returns:

The equivalence class to transcript dict, the equivalence class to gene dict, and the gene to equivalence class dict.

Return type:

Tuple[Dict[str, str], Dict[str, str], Dict[str, str]]