multivelo.recover_dynamics_chrom function output .layers[["fit_state']]

[siyao-liu]

Hi,

Can someone please tell me which states are 0s, 1s, 2s, and 3s refer to from the output of multivelo.recover_dynamics_chrom function output .layers[["fit_state']]? Thank you!

[danielee0707]

State 0s, 1s, 2s, and 3s refer to different orders of states depending on a gene's model assignment. For a Model 1 gene, the order is (chromatin priming phase) -> (coupled induction phase) -> (decoupled repression phase: chromatin closing, transcription induction) -> (stably repression phase) For a Model 2 gene, the order is (chromatin priming phase) -> (coupled induction phase) -> (decoupled repression phase: chromatin opening, transcription repression) -> (stably repression phase) You can find the model assignment of each gene in adata_result.var.fit_model after fitting the model. You can refer to Fig 1 of the manuscript for detailed explanations.

[siyao-liu]

@danielee0707 thanks for your response. So, state 0 = primed, 1=coupled on, 2=decoupled, 3=coupled off?

[danielee0707]

Yes, that's correct.