# Correcting the Coverage of Credible Sets from Bayesian Genetic Fine Mapping

## Documentation for package ‘corrcoverage’ version 1.1.0

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

## Help Pages

.zj_abf | Internal function: Simulate nrep ABFs from joint Z-score vector
.zj_pp | Simulate posterior probabilities of causality from joint Z-score vector
approx.bf.p | Find approx. Bayes factors (ABFs)
bf_func | Calculate ABFs from Z scores
cor2 | Correlation matrix of SNPS
corrcov | Corrected coverage estimate using Z-scores and MAFs
corrcov_bhat | Corrected coverage estimate using estimated effect sizes and their standard errors
corrcov_CI | Confidence interval for corrected coverage estimate using Z-scores and MAFs
corrcov_CI_bhat | Confidence interval for corrected coverage estimate using estimated effect sizes and their standard errors
corrcov_nvar | Corrected coverage estimate using Z-scores and MAFs (fixing nvar)
corrcov_nvar_bhat | Corrected coverage estimate using estimated effect sizes and their standard errors (fixing nvar)
corrected_cov | Corrected coverage estimate of the causal variant in the credible set
corrected_cs | Corrected credible set using Z-scores and MAFs
corrected_cs_bhat | Corrected credible set using estimated effect sizes and their standard errors
credset | Credible set of genetic variants
credsetC | Credible set of variants from matrix of PPs
credsetmat | Obtain credible sets from a matrix of posterior probabilities
est_mu | Estimate the true effect at the causal variant using Z-scores and MAFs
est_mu_bhat | Estimate the true effect at the causal variant using estimated effect sizes and their standard errors
logsum | logsum
logsum_matrix | logsum rows of a matrix
ppfunc | Find PPs of SNPs from Z-scores
ppfunc.mat | Find PPs of SNPs from matrix of Z-scores
prop_cov | Proportion of credible sets containing the causal variant
pvals_pp | Find PPs for SNPs and null model from P-values and MAFs
Var.data.cc | Variance of the estimated effect size for case-control data
z0_pp | Find PPs for SNPs and null model from Z-scores and MAFs
zj_pp | Simulate posterior probabilities of causality from joint Z-score vector
z_sim | Simulate marginal Z-scores from joint Z-score vector