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Correlation networks #256

Closed d-callan closed 4 months ago

d-callan commented 4 months ago

in an effort to get to a place where we can filter our networks here based on correlation coef and pvalue, weve introduced some dedicated classes for networks specifically representing correlations.

d-callan commented 4 months ago

hmmmm. not sure i added the thresholds used to the response yet..

d-callan commented 4 months ago

Can you please explain the value of the extra BaseNetwork class? I don't follow why CorrelationNetwork can't just inherit from Network

Network has type LinkList for its links slot, and we want CorrelationLinkList specifically for a CorrelationNetwork. this strategy guarantees us that. BaseNetwork, bc it inherits from VIRTUAL, is not implementable. it serves only as a thing to hang other classes and relevant methods etc off of.

I'd like to voice my general disdain for functions with argument names "object" or "x" and are more than 4 lines long :) It makes the code so much harder to follow for me.

yea. it bothers me sometimes too.. unfortunately the arg/ docs i think have to keep saying 'object' or similar for the case of the S4 methods... but we could rapidly rename them within the methods maybe in the future..