.bf_em_coloc_pi0        Multi-INTACT EM algorithm fixed-point function.
.bf_loglik_coloc        Multi-INTACT EM algorithm log-likelihood
                        function.
.bf_weighted_sum_coloc
                        Helper function for EM algorithm to compute
                        weighted sum of Bayes factors.
.em_est                 Compute gene set enrichment estimates.
.enrich_bootstrap_se    Compute bootstrap standard errors for alpha
                        MLEs.
.enrich_res             Compute gene set enrichment estimates with
                        standard errors.
.logistic_em            A fixed-point mapping for the
                        expectation-maximization algorithm. Used as an
                        argument for fixptfn in the squarem function.
.logistic_em_nopseudo   Similar to logistic_em(), but does not use
                        pseudocounts to stablize the algorithm.
.logistic_loglik        A log likelihood function for the
                        expectation-maximization algorithm. Used as an
                        argument for objfn in the squarem function.
.multi_em_posteriors    Compute gene product relevance probabilities
                        using prior parameter estimates and Bayes
                        factors.
.multi_prior_estimation
                        Compute Multi-INTACT prior parameter estimates
                        and gene product relevance probabilities.
.pi1_fun                Estimate pi1 from TWAS scan z-scores.
.wakefield_bf_z_ln      A function to compute log Bayes factors from
                        z-statistics using the Wakefield formula
chisq_sumstat           Compute a gene-level multivariate Wald
                        chi-square statistic using summary-level
                        genetic association and LD data.
expit                   Transform a gene colocalization probability
                        (GLCP) to a prior to be used in the evidence
                        integration procedure. There are four prior
                        function options, including expit, linear,
                        step, and expit-linear hybrid.
exprwt_sumstats         TWAS weights for a simulated gene.
fdr_rst                 Bayesian FDR control for INTACT output
gene_set_list           Simulated gene set list.
hybrid                  Transform a gene colocalization probability
                        (GLCP) to a prior to be used in the evidence
                        integration procedure. There are four prior
                        function options, including expit, linear,
                        step, and expit-linear hybrid.
intact                  Compute the posterior probability that a gene
                        may be causal, given a gene's TWAS scan z-score
                        (or Bayes factor) and colocalization
                        probability.
intactGSE               Perform gene set enrichment estimation and
                        inference, given TWAS scan z-scores and
                        colocalization probabilities.
ld_sumstats             LD correlation matrix from a simulated data
                        set.
linear                  Transform a gene colocalization probability
                        (GLCP) to a prior to be used in the evidence
                        integration procedure. There are four prior
                        function options, including expit, linear,
                        step, and expit-linear hybrid.
multi_intact            Compute Multi-INTACT prior parameter estimates
                        and gene product relevance probabilities.
multi_simdat            Simulated TWAS, PWAS, and pairwise
                        colocalization summary data.
protwt_sumstats         PWAS weights for a simulated gene.
simdat                  Simulated TWAS and colocalization summary data.
step                    Transform a gene colocalization probability
                        (GLCP) to a prior to be used in the evidence
                        integration procedure. There are four prior
                        function options, including expit, linear,
                        step, and expit-linear hybrid.
z_sumstats              TWAS and PWAS z-score for a simulated gene.
