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Add AnnotatedPhenotypeSimulator #2

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2 of 5 tasks
shz9 opened this issue Oct 29, 2021 · 0 comments
Open
2 of 5 tasks

Add AnnotatedPhenotypeSimulator #2

shz9 opened this issue Oct 29, 2021 · 0 comments
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enhancement New feature or request

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@shz9
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shz9 commented Oct 29, 2021

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:

  • Remove annotation_weights property (as well as other related methods) from GWASimulator.
  • 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.
@shz9 shz9 added the enhancement New feature or request label Oct 29, 2021
@shz9 shz9 changed the title Add FunctionalGWASimulator Add AnnotatedPhenotypeSimulator May 22, 2024
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