The current PhenotypeSimulator class has some functionality for simulating with annotations. We need to remove those functionalities and embed them in a new class AnnotatedPhenotypeSimulator that inherits from PhenotypeSimulator and incorporates annotations in simulate_mixture_assignments and simulate_betas.
Tasks:
[x] Remove annotation_weights property (as well as other related methods) from GWASimulator.
[x] Create AnnotatedPhenotypeSimulator class
[ ] In AnnotatedPhenotypeSimulator, overwrite the simulate_mixture_assignment method to incorporate annotations.
[ ] In AnnotatedPhenotypeSimulator, overwrite the simulate_betas method to incorporate annotations.
Additionally, we need to figure out two things:
[ ] How to simulate betas according to user-defined enrichments for each (or some) annotation classes.
The current
PhenotypeSimulatorclass has some functionality for simulating with annotations. We need to remove those functionalities and embed them in a new classAnnotatedPhenotypeSimulatorthat inherits fromPhenotypeSimulatorand incorporates annotations insimulate_mixture_assignmentsandsimulate_betas.Tasks:
annotation_weightsproperty (as well as other related methods) fromGWASimulator.AnnotatedPhenotypeSimulatorclassAnnotatedPhenotypeSimulator, overwrite thesimulate_mixture_assignmentmethod to incorporate annotations.AnnotatedPhenotypeSimulator, overwrite thesimulate_betasmethod to incorporate annotations.Additionally, we need to figure out two things: