preprocess.prepare_transcriptomic

preprocess.prepare_transcriptomic(
    data,
    *,
    orthologues=None,
    genes=None,
    centre=True,
)

Run the whole chain, in order, recording each step.

Parameters

Name	Type	Description	Default
orthologues	dict[str, str] | pd.Series | None	Source gene id to the model’s gene id, for scoring one species with a model fitted in another. Applied first, and one-to-one only: a many-to-one map would silently sum paralogues into one column, and which paralogue a clock’s coefficient refers to is not recoverable afterwards.	None
genes	list[str] | None	The model’s gene list. Absent genes are padded with NaN rather than dropped, so coverage reporting downstream sees them missing instead of never knowing they were expected.	None
centre	bool	The per-dataset median centring. False leaves it out, which is only right if you are going to do it yourself over the correct cohort.	True