Package index • cophescan

CoPheScan with fixed priors

per.snp.priors(): per.snp.priors
adjust_priors(): adjust_priors
hypothesis.priors(): hypothesis.priors
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
combine.bf(): combine.bf
cophe.multitrait(): Run cophescan on multiple traits at once
summary(<cophe>): print the summary of results from cophescan single or susie
multitrait.simplify(): Simplifying the output obtained from cophe.multitrait, cophe.single or cophe.susie
logsum(): logsum

run_metrop_priors(): Run the hierarchical Metropolis Hastings model to infer 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)
get_posterior_prob(): Calculation of the posterior prob of Hn, Ha and Hc
get_beta(): Extract beta and p-values of queried variant
sample_alpha(): sample alpha
sample_beta(): sample beta
sample_gamma(): sample gamma
logd_alpha(): dnorm for alpha
logd_beta(): dgamma for beta
logd_gamma(): dgamma for gamma
loglik(): Log likelihood calculation
logpost(): Log posterior calculation
logsumexp(): Log sum
metrop_run(): Run the hierarchical mcmc model to infer priors
pars2pik(): Conversion of parameters alpha, beta and gamma to pnk, pak and pck
piks(): List of priors: pn, pa and pc over all iterations
posterior_prob(): List of posterior probabilities: Hn, Ha and Hc over all iterations
logpriors(): Calculate log priors
pars_init(): Initiate parameters alpha, beta and gamma
propose(): Proposal distribution
target(): Target distribution

plot_trait_manhat(): Plot region Manhattan for a trait highlighting the queried variant
cophe_plot(): cophe_plots showing the Ha and Hc of all traits and labelled above the specified threshold
cophe_heatmap(): Heatmap of multi-trait cophescan results
prepare_plot_data(): Prepare data for plotting