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| 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' |