# Wrapper Functions for GUESS

## Documentation for package ‘R2GUESS’ version 2.0

- DESCRIPTION file.

## Help Pages

R2GUESS-package | Sparse Bayesian variable selection method for linear regression based analysis of possibly multivariate outcomes.
Analysis.permutation | Computing the FDR-controlled level for the significance of the MPPI
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
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
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.
MAP.file | MAP file describing genotypes from the rats experiment.
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
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
plotMPPI | Plots the marginal posterior probability of inclusion (MPPI) for each predictor
plotvariable | Visualisation of the best models
Postprocess.R2GUESS | Performs posterior inference from an interrupted 'R2GUESS' run.
print.ESS | Provides a 'print' method for class 'ESS'
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
Resume.R2GUESS | Function resuming an interrupted 'R2GUESS' run
sample.beta | Posterior distribution of the regression coefficients for a chosen model
summary.ESS | 'summary' method for class 'ESS'