Analysis.permutation    Computing the FDR-controlled level for the
                        significance of the MPPI
Extend.R2GUESS          Extends an already finished 'R2GUESS' run for
                        an extra user-defined number of iterations
FDR.permutation         Performs parallel permuted runs of 'R2GUESS'
                        and returns the empirical FDR-controlled level
                        for the significance of the MPPI
MAP.file                MAP file describing genotypes from the rats
                        experiment.
Postprocess.R2GUESS     Performs posterior inference from an
                        interrupted 'R2GUESS' run.
R2GUESS                 Wrapper function that reads the input files and
                        parameter values required by GUESS, runs the
                        C++ code from R and stores the main GUESS
                        output in an 'ESS' object
R2GUESS-package         Sparse Bayesian variable selection method for
                        linear regression based analysis of possibly
                        multivariate outcomes.
Resume.R2GUESS          Function resuming an interrupted 'R2GUESS' run
as.ESS.object           Compiles the main input and output files from a
                        previous run of 'R2GUESS' and creates an ESS
                        object.
boxplotbeta             Draws boxplots of the posterior distribution of
                        regression coefficient(s) for a given predictor
check.convergence       Diagnostic plots for the evaluation of the
                        convergence of the algorithm
data.X                  Data set compiling genotype data for 29 rats.
data.Y.Hopx             Data set compiling gene expression levels (HOPX
                        gene) for 29 rats.
example.as.ESS.object   Function creating an 'ESS' object from the
                        example files contained in the package
get.g.sweep             Internal function used to generate the
                        regression coefficients. This function extracts
                        the values of the shrinkage factor g for a
                        given model specified by its ranked posterior
                        probability
get.sweep.best.model    Internal function used to generate the
                        regression coefficients. This function extracts
                        the sweep(s) for which each selected models has
                        been visited along the MCMC run.
pairwise.correlation    Calculates and plots the pairwise correlation
                        between outcomes
plot.ESS                Provides diagnostic plots to assess the
                        convergence of the MCMC procedure along the run
plotMPPI                Plots the marginal posterior probability of
                        inclusion (MPPI) for each predictor
plotcim                 Clustered Image Maps (CIMs) (heat maps)
plotcim.explore         Plots a cluster image mapping of correlations
                        between outcomes and all predictors
plotmodel               Visualisation of the proximity between best
                        models
plotvariable            Visualisation of the best models
print.ESS               Provides a 'print' method for class 'ESS'
sample.beta             Posterior distribution of the regression
                        coefficients for a chosen model
summary.ESS             'summary' method for class 'ESS'
