Correcting the Coverage of Credible Sets from Bayesian Genetic Fine Mapping

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Documentation for package ‘corrcoverage’ version 1.2.1

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

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