cojam: Merge two 'JAM' models

Description Usage Arguments Value

Description

Combines samples from the posterior model space of two JAM models, allowing posterior inference about colocalisation, i.e. about the existence of one or more shared variants that are associated with both outcome traits.

Usage

1
cojam(jam_res_1, jam_res_2)

Arguments

jam_res_1

A R2BGLiMS_Results-class object, from running JAM for trait 1.

jam_res_2

A R2BGLiMS_Results-class object, from running JAM for trait 2.

Value

A list containing the following elements:

bayes_factor

Bayes Factor for H4 versus H3.

posterior_overlap

Posterior probability of H4 U H3.

model_info

Extra info for other functions / post-processing:

models_grid

All sampled configurations (joint JAM models) and their posterior counts.

implied_prior_odds_43

Prior odds of H4 versus H3 that would have been implied under an assumption of independence between traits. Provided as a sanity check for user-supplied priors, which should usually promote H4 vs H3 (i.e. user supplied prior_odds_43 should usually be greater than implied_prior_odds_43).


simisc/cojam documentation built on Dec. 31, 2020, 7:26 a.m.