What the the difference between fit_GRN_for_simulation, fit_GRN_for_network_analysis?

[swapnilkeshari]

Hello,
While I was going throught the code I wanted to understand what is the difference between these two functions? Since on the face of it both the functions seems to do very similar things with some nuances.

From my understanding of the workflow [Caveat: 2k/10k/ etc. are for ex. as they were in the tutorial]

1. we create a link object, which when filtered to top 2k edges gets us the network stats and has coef & pvalues for each edge.
2. Following this, we again do filter_links() to get top 10k and then do oracle.fit_GRN_for_simulation() which does second round of fitting. but this time I only get the coefficients from oracle.coef_matrix_per_cluster. but no p_values associated with the fit.

Lastly if we are doing KO on the second fit, shouldn't that be considered the "final GRN" and network stats be generated for those? How can I get the links object after the second fit of oracle?