troutpy.pp.compute_extracellular_counts

troutpy.pp.compute_extracellular_counts#

troutpy.pp.compute_extracellular_counts(data_extracell)#

Compute observed and expected transcript counts, log fold-ratio over baseline, and codeword category per gene for extracellular transcripts.

Parameters:

data_extracell (pandas.DataFrame) – DataFrame of extracellular transcripts. Must contain a feature_name column with gene identifiers and a codeword_category column with probe category labels.

Returns:

-extracellular_counts (DataFrame) DataFrame indexed by gene name with columns:

  • observed : int — raw transcript count per gene.

  • expected : int — uniform expected count (total / number of genes).

  • fold_ratio : float — log(observed / expected).

  • codeword_category : str — probe category for each gene.

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