reconstruction.ecoli.dataclasses.process.transcription_regulation
SimulationData for transcription regulation
- class reconstruction.ecoli.dataclasses.process.transcription_regulation.TranscriptionRegulation(raw_data, sim_data)[source]
Bases:
object
SimulationData for transcription regulation
- _build_lookups(raw_data)[source]
Builds dictionaries for mapping transcription factor abbreviations to their RNA IDs, and to their active form.
- get_delta_prob_matrix(dense=False, ppgpp=False)[source]
Returns the delta probability matrix mapping the promoter binding effect of each TF to each gene.
- Parameters:
dense – If True, returns a dense matrix, otherwise csr sparse
ppgpp – If True, normalizes delta probabilities to be on the same scale as ppGpp normalized probabilities since delta_prob is calculated based on basal_prob which is not normalized to 1
- Returns:
- matrix of probabilities changes expected with a TF
binding to a promoter for each gene (n genes, m TFs)
- Return type:
delta_prob