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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

21

Version

2.0

License

GPL-3

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Repository

https://github.com/ImperialCollegeLondon/R2GUESS

Maintainer

Gianluca Campanella

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 set compiling genotype data for 29 rats.

get.best.models

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

Clustered Image Maps (CIMs) (heat maps)

Plots the marginal posterior probability of inclusion (MPPI) for each predictor

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

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

Visualisation of the best models

Provides a print method for class ESS

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.

Posterior distribution of the regression coefficients for a chosen model

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.

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

summary method for class ESS

check.convergence

Diagnostic plots for the evaluation of the convergence of the algorithm

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.

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

Function resuming an interrupted R2GUESS run

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

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 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

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