# Adaptation of the Coloc Method for PheWAS

## Documentation for package ‘cophescan’ version 1.4.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

cophescan-package | The 'cophescan' package.
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 intensive)
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 (memory intensive)
combine.bf | combine.bf
cophe.hyp.predict | Predict cophescan hypothesis for tested associations
cophe.multitrait | Run cophescan on multiple traits at once
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
cophescan | The 'cophescan' package.
cophe_heatmap | Heatmap of multi-trait cophescan results
cophe_multi_trait_data | Simulated multi-trait data
cophe_plot | cophe_plots showing the Ha and Hc of all traits and labelled above the specified threshold
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', 'cophe.single' or 'cophe.susie'
pars2pik | Conversion of parameters alpha, beta and gamma to pnk, pak and pck
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 variant
posterior_prob | List of posterior probabilities: Hn, Ha and Hc over all iterations
prepare_plot_data | Prepare data for plotting
propose | Proposal distribution
run_metrop_priors | Run the hierarchical Metropolis Hastings model to infer priors
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