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R2GUESS

Installation

You can install the released version of R2GUESS from CRAN with:

install.packages("R2GUESS")

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Install

install.packages('R2GUESS')

Monthly Downloads

89

Version

2.0

License

GPL-3

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Last Published

December 20th, 2018

Functions in R2GUESS (2.0)

pairwise.correlation

Calculates and plots the pairwise correlation between outcomes
example.as.ESS.object

Function creating an ESS object from the example files contained in the package
data.X

Data set compiling genotype data for 29 rats.
get.best.models

Internal function used to read in R the result of the best model
plotcim

Clustered Image Maps (CIMs) (heat maps)
plotMPPI

Plots the marginal posterior probability of inclusion (MPPI) for each predictor
data.Y.Hopx

Data set compiling gene expression levels (HOPX gene) for 29 rats.
plot.ESS

Provides diagnostic plots to assess the convergence of the MCMC procedure along the run
plotvariable

Visualisation of the best models
print.ESS

Provides a print method for class ESS
R2GUESS.perm

Internal function used for the parallel computation on the permutation procedure for the calibration of the FDR threshold regarding the significance of the MPPI. This function run GUESS on permutation sample.
sample.beta

Posterior distribution of the regression coefficients for a chosen model
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.
boxplotbeta

Draws boxplots of the posterior distribution of regression coefficient(s) for a given predictor
summary.ESS

summary method for class ESS
check.convergence

Diagnostic plots for the evaluation of the convergence of the algorithm
plotmodel

Visualisation of the proximity between best models
plotcim.explore

Plots a cluster image mapping of correlations between outcomes and all predictors
summarybest.model

Internal function used for the summary.ESS function.
wrapper

Internal function used for the parallel computation on the permutation procedure for the calibration of the FDR threshold regarding the significance of the MPPI
Resume.R2GUESS

as.ESS.object

Compiles the main input and output files from a previous run of R2GUESS and creates an ESS object.
FDR.permutation

Performs parallel permuted runs of R2GUESS and returns the empirical FDR-controlled level for the significance of the MPPI
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
MAP.file

MAP file describing genotypes from the rats experiment.
Postprocess.R2GUESS

Performs posterior inference from an interrupted R2GUESS run.
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
Extend.R2GUESS

Extends an already finished R2GUESS run for an extra user-defined number of iterations