Add the option for a random GRN

dgoldsb / synergy-jointpdf

0 stars 0 forks source link

Add the option for a random GRN #12

Closed dgoldsb closed 5 years ago

dgoldsb commented 7 years ago

[ ] Make connections sparse
[ ] Start with a networkx network, use build in function for right properties
[x] Generate rules
[x] Add a correlation matrix
[x] Finish with a system that can be exported to JSON.

dgoldsb commented 7 years ago

The first generator can be pretty suboptimal, I should first just try to get some results.

dgoldsb commented 7 years ago

For the first generator I am just going to pick the inputs and outputs of the rules uniformly, as well as the number of links. Especially when we are dealing with motifs of 3 to 4 genes there is not much of a point in generating Barabasi-Albert networks (yet).

dgoldsb commented 7 years ago

I need to reconsider the generator a bit, to make sure it does not create things that are not networks. This includes looking at the possible rules again.

dgoldsb commented 7 years ago

I improved this function: I consider all possible edges, and select a rule for a sample without replacement from these edges.