Man pages for jean997/cause
CAUSE: Causal Analysis Using Summary Effect Estimates
| adapt2_grid | Adaptive grid estimation of posteriors |
| cause | CAUSE |
| cause_download_example_gwas_data | Download GWAS data to use in examples |
| cause_grid_adapt | CAUSE posterior density estimation |
| est_cause_params | Estimate CAUSE Nuisance Parameters |
| est_cause_params_future | Estimate CAUSE Nuisance Parameters |
| eta_gamma_prior | Prior variance for gamma and eta |
| gwas_format | Convert GWAS summary statistics to a standard format |
| gwas_merge | Format data for CAUSE |
| in_sample_elpd_loo | Estimate delta elpd for pairs of models |
| ld_prune | Prune variants for LD |
| loglik | Calculate likelihood - version 7 |
| loglik_ij | Calculate likelihood of (beta_hat_1[j], beta_hat_2[j])) given... |
| loglik_loo | Calculate likelihood matrix for LOO (SNPs by posterior... |
| loglik_mat | Calculate likelihood matrix - version 7 |
| loglik_samps_Z0 | Calculate likelihood matrix for LOO (SNPs by posterior... |
| loglik_samps_Z1 | Calculate likelihood matrix for LOO (SNPs by posterior... |
| map_pi_rho | Estimate pi and mixture proportions under null model |
| map_pi_rho_nonnull | Estimate pi and mixture proportions under a specified model |
| map_pi_rho_nonnull_eqg | Estimate pi and mixture proportions under a specified model |
| map_pi_rho_nonnull_fixed | Estimate pi and mixture proportions under a specified model |
| map_pi_rho_nonnull_geq | Estimate pi and mixture proportions under a specified model |
| map_pi_rho_nonnull_qge | Estimate pi and mixture proportions under a specified model |
| new_cause_data | Create a new cause_data object |
| new_cause_data_fit | Create a new cause_data_fit object |
| plot.cause | Plot CAUSE |
| plot.cause_post | Plot posteriors for one CAUSE fit |
| print.cause_summary | Print CAUSE Summary |
| print.summary_cause_post | Print CAUSE fit Summary |
| recompute_elpd_table | Recompute elpd table for a CAUSE fit that is already computed |
| samp_from_grid | Sample from grid approximation of posterior distribuitions |
| setup_cause_pipeline | Set up analysis directory for pairs of GWAS summary... |
| setup_gwas_pairs | Set up analysis directory for pairs of GWAS summary... |
| step_quantile | Quantile of a step pdf |
| summary.cause | Summarize CAUSE Results |
| summary.cause_post | Summarize CAUSE Results for a single fit |
| Z_post | Posterior probability of acting through U |
