CAUSE: Causal Analysis Using Summary Effect Estimates

cause_grid_approx | CAUSE with grid approximation and fixed rho |

cause_grid_approx_v7 | CAUSE with grid approximation and fixed rho |

cause_mh_v7 | Estimate posteriors for version 7 model |

fit_cause | Fit CAUE |

get_map | Try to find the MAP using coordinate descent |

get_map_old | Try to find the MAP using coordinate descent |

in_sample_elpd_loo | Estimate delta elpd for pairs of models |

ld_prune_pval_format3 | Rank SNPs by pval, prune for LD |

ld_prune_pval_format4 | Rank SNPs by pval, prune for LD |

ll_v4 | Calculate likelihood - version 4 |

ll_v4_ij | Calculate likelihood of (beta_hat_1[j], beta_hat_2[j])) given... |

ll_v4_loo | Calculate likelihood matrix for LOO (SNPs by posterior... |

ll_v4_mat | Calculate likelihood matrix - version 4 |

ll_v4_single | Calculate likelihood - version 4, not in parallel |

ll_v6 | Calculate likelihood - version 6 |

ll_v6_ij | Calculate likelihood of (beta_hat_1[j] beta_hat_2(j)) given... |

ll_v6_mat | Calculate likelihood matrix - version 6 |

ll_v7 | Calculate likelihood - version 7 |

ll_v7_ij | Calculate likelihood of (beta_hat_1[j], beta_hat_2[j])) given... |

ll_v7_loo | Calculate likelihood matrix for LOO (SNPs by posterior... |

ll_v7_mat | Calculate likelihood matrix - version 7 |

ll_v7_samps_Z0 | Calculate likelihood matrix for LOO (SNPs by posterior... |

ll_v7_samps_Z1 | Calculate likelihood matrix for LOO (SNPs by posterior... |

map_pi_rho | Try to find the MAP for pi and rho using coordinate descent |

qqthin | Plot qq-plot from p-values with shading |

rnormalmix | Simulate from a normal mixture distribution |

sherlock1 | Calculate Bayes Factor for original Sherlock |

sherlockAsh | sherlockAsh |

simulate_summary_statistics | Simulate summary statistics |

top_snps_pval_ld | Rank SNPs by pval, prune for LD |

top_snps_pval_ld2 | Rank SNPs by pval, prune for LD |

top_snps_pval_ld2_new | Rank SNPs by pval, prune for LD |

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