| adjust_priors | adjust_priors |
| average_piks | Average of priors: pnk, pak and pck |
| average_piks_list | Average of priors: pnk, pak and pck from list (memory... |
| average_posterior_prob | Average of posterior probabilities: Hn, Ha and Hc |
| average_posterior_prob_list | Average of posterior probabilities: Hn, Ha and Hc from list... |
| combine.bf | combine.bf |
| cophe.bf_bf | extract data through Bayes factors |
| cophe_heatmap | Heatmap of multi-trait cophescan results |
| cophe.hyp.predict | Predict cophescan hypothesis for tested associations |
| cophe.multitrait | Run cophescan on multiple traits at once |
| cophe_multi_trait_data | Simulated multi-trait data |
| cophe_plot | cophe_plots showing the Ha and Hc of all traits and labelled... |
| cophe.prepare.dat.single | Prepare data for cophe.single |
| cophe.prepare.dat.susie | Prepare data for 'cophe.susie' |
| cophescan-package | The 'cophescan' package. |
| cophe.single | Bayesian cophescan analysis using Approximate Bayes Factors |
| cophe.single.lbf | cophe.single.lbf |
| cophe.susie | run 'cophe.susie' using susie to detect separate signals |
| cophe.susie.lbf | cophe.susie.lbf |
| get_beta | Extract beta and p-values of queried variant |
| get_posterior_prob | Calculation of the posterior prob of Hn, Ha and Hc |
| Hc.cutoff.fdr | Estimate the Hc.cutoff for the required FDR |
| hypothesis.priors | hypothesis.priors |
| logd_alpha | dnorm for alpha |
| logd_beta | dgamma for beta |
| logd_gamma | dgamma for gamma |
| loglik | Log likelihood calculation |
| logpost | Log posterior calculation |
| logpriors | Calculate log priors |
| logsum | logsum |
| logsumexp | Log sum |
| metrop_run | Run the hierarchical mcmc model to infer priors |
| multitrait.simplify | Simplifying the output obtained from 'cophe.multitrait',... |
| pars2pik | Conversion of parameters alpha, beta and gamma to pnk, pak... |
| pars_init | Initiate parameters alpha, beta and gamma |
| per.snp.priors | per.snp.priors |
| piks | List of priors: pn, pa and pc over all iterations |
| plot_trait_manhat | Plot region Manhattan for a trait highlighting the queried... |
| posterior_prob | List of posterior probabilities: Hn, Ha and Hc over all... |
| prepare_plot_data | Prepare data for plotting |
| propose | Proposal distribution |
| run_metrop_priors | Run the hierarchical Metropolis Hastings model to infer... |
| sample_alpha | sample alpha |
| sample_beta | sample beta |
| sample_gamma | sample gamma |
| summary.cophe | print the summary of results from cophescan single or susie |
| target | Target distribution |
