R2GUESS: Wrapper Functions for GUESS

Wrapper functions for GUESS, a GPU-enabled sparse Bayesian variable selection method for linear regression based analysis of possibly multivariate/correlated outcomes.

AuthorGianluca Campanella [cre], Benoit Liquet [aut], Marc Chadeau-Hyam [aut], Leonardo Bottolo [ctb], Sylvia Richardson [ctb]
Date of publication2016-01-26 15:19:28
MaintainerGianluca Campanella <gianluca@campanella.org>
LicenseGPL (>= 2)
Version1.7

View on CRAN

Man pages

Analysis.permutation: Computing the FDR-controlled level for the significance of...

as.ESS.object: Compiles the main input and output files from a previous run...

boxplotbeta: Draws boxplots of the posterior distribution of regression...

check.convergence: Diagnostic plots for the evaluation of the convergence of the...

data.X: Data set compiling genotype data for 29 rats.

data.Y.Hopx: Data set compiling gene expression levels (HOPX gene) for 29...

example.as.ESS.object: Function creating an 'ESS' object from the example files...

Extend.R2GUESS: Extends an already finished 'R2GUESS' run for an extra...

FDR.permutation: Performs parallel permuted runs of 'R2GUESS' and returns the...

get.best.models: Internal function used to read in R the result of the best...

get.g.sweep: Internal function used to generate the regression...

get.sweep.best.model: Internal function used to generate the regression...

MAP.file: MAP file describing genotypes from the rats experiment.

pairwise.correlation: Calculates and plots the pairwise correlation between...

plotcim: Clustered Image Maps (CIMs) (heat maps)

plotcim.explore: Plots a cluster image mapping of correlations between...

plot.ESS: Provides diagnostic plots to assess the convergence of the...

plotmodel: Visualisation of the proximity between best models

plotMPPI: Plots the marginal posterior probability of inclusion (MPPI)...

plotvariable: Visualisation of the best models

Postprocess.R2GUESS: Performs posterior inference from an interrupted 'R2GUESS'...

print.ESS: Provides a 'print' method for class 'ESS'

R2GUESS: Wrapper function that reads the input files and parameter...

R2GUESS-package: Sparse Bayesian variable selection method for linear...

R2GUESS.perm: Internal function used for the parallel computation on the...

Resume.R2GUESS: Function resuming an interrupted 'R2GUESS' run

sample.beta: Posterior distribution of the regression coefficients for a...

summarybest.model: Internal function used for the summary.ESS function.

summary.ESS: 'summary' method for class 'ESS'

wrapper: Internal function used for the parallel computation on the...

Files in this package

R2GUESS
R2GUESS/inst
R2GUESS/inst/Output
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_output_marg_prob_incl.txt
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_output_log_cond_post_prob_history.txt
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_output_g_history.txt
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_output_g_adaptation_history.txt
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_features.txt
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_output_fast_scan_history.txt
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_output_all_exchange_history.txt
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_resume.txt
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_output_n_models_visited_history.txt
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_output_temperature_history.txt
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_output_model_size_history.txt
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_output_gibbs_history.txt
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_output_delayed_rejection_history.txt
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_output_time_monitor.txt
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_random.rng
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_output_marg_prob_incl_mc.txt
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_output_best_visited_models.RData
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_output_models_history.txt
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_log
R2GUESS/inst/Output/Example-GUESS-Y-Hopx-command-C.txt
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_output_best_visited_models.txt
R2GUESS/inst/Output/Example-GUESS-Y-Hopx_output_cross_over_history.txt
R2GUESS/inst/CITATION
R2GUESS/inst/Input
R2GUESS/inst/Input/data-Y-ALL-C-CODE.txt
R2GUESS/inst/Input/data-X-C-CODE.txt
R2GUESS/inst/extdata
R2GUESS/inst/extdata/Par_file_example_Hopx.xml
R2GUESS/configure.ac
R2GUESS/src
R2GUESS/src/Main
R2GUESS/src/Main/GUESS.cc
R2GUESS/src/install.libs.R
R2GUESS/src/Classes
R2GUESS/src/Classes/Double_Matrices.h
R2GUESS/src/Classes/Double_Matrices.cc
R2GUESS/src/Classes/String_Matrices.h
R2GUESS/src/Classes/Move_monitor.cc
R2GUESS/src/Classes/Double_Matrices_cont.h
R2GUESS/src/Classes/g_AdMH.h
R2GUESS/src/Classes/String_Matrices.cc
R2GUESS/src/Classes/Temperatures.cc
R2GUESS/src/Classes/Prior_param.h
R2GUESS/src/Classes/g_AdMH.cc
R2GUESS/src/Classes/Int_Matrices.h
R2GUESS/src/Classes/DR.cc
R2GUESS/src/Classes/CM.h
R2GUESS/src/Classes/Move_monitor.h
R2GUESS/src/Classes/DR.h
R2GUESS/src/Classes/Double_Matrices_cont.cc
R2GUESS/src/Classes/CM.cc
R2GUESS/src/Classes/Int_Matrices_var_dim.cc
R2GUESS/src/Classes/Int_Matrices.cc
R2GUESS/src/Classes/Temperatures.h
R2GUESS/src/Classes/Prior_param.cc
R2GUESS/src/Classes/Int_Matrices_var_dim.h
R2GUESS/src/Makevars.in
R2GUESS/src/Makevars.win
R2GUESS/src/Routines
R2GUESS/src/Routines/post_processing.cc
R2GUESS/src/Routines/rand.h
R2GUESS/src/Routines/cond_post.cc
R2GUESS/src/Routines/xml_file_read.cc
R2GUESS/src/Routines/matrix_handling.h
R2GUESS/src/Routines/cond_post.h
R2GUESS/src/Routines/post_processing.h
R2GUESS/src/Routines/matrix_handling.cc
R2GUESS/src/Routines/rand.cc
R2GUESS/src/Routines/moves.h
R2GUESS/src/Routines/regression.cc
R2GUESS/src/Routines/guess_math.h
R2GUESS/src/Routines/moves.cc
R2GUESS/src/Routines/dyn_name.cc
R2GUESS/src/Routines/xml_file_read.h
R2GUESS/src/Routines/struc.h
R2GUESS/src/Routines/regression.h
R2GUESS/src/Routines/dyn_name.h
R2GUESS/src/Routines/guess_math.c
R2GUESS/NAMESPACE
R2GUESS/data
R2GUESS/data/MAP.file.rda
R2GUESS/data/data.Y.Hopx.rda
R2GUESS/data/data.X.rda
R2GUESS/R
R2GUESS/R/R2GUESS.R R2GUESS/R/plotMPPI.R R2GUESS/R/Extend.R2GUESS.R R2GUESS/R/R2GUESS-package.R R2GUESS/R/print.ESS.R R2GUESS/R/R2GUESS.perm.R R2GUESS/R/Analysis.permutation.R R2GUESS/R/Resume.R2GUESS.R R2GUESS/R/sample.beta.R R2GUESS/R/get.g.sweep.R R2GUESS/R/plotcim.R R2GUESS/R/plotmodel.R R2GUESS/R/as.ESS.object.R R2GUESS/R/plotvariable.R R2GUESS/R/summary.ESS.R R2GUESS/R/get.best.models.R R2GUESS/R/check.convergence.R R2GUESS/R/FDR.permutation.R R2GUESS/R/summarybest.model.R R2GUESS/R/plotcim.explore.R R2GUESS/R/Postprocess.R2GUESS.R R2GUESS/R/wrapper.R R2GUESS/R/pairwise.correlation.R R2GUESS/R/plot.ESS.R R2GUESS/R/get.sweep.best.model.R R2GUESS/R/example.as.ESS.object.R R2GUESS/R/boxplotbeta.R
R2GUESS/MD5
R2GUESS/DESCRIPTION
R2GUESS/configure
R2GUESS/man
R2GUESS/man/plotcim.explore.Rd R2GUESS/man/plot.ESS.Rd R2GUESS/man/pairwise.correlation.Rd R2GUESS/man/plotvariable.Rd R2GUESS/man/summarybest.model.Rd R2GUESS/man/get.best.models.Rd R2GUESS/man/R2GUESS.perm.Rd R2GUESS/man/check.convergence.Rd R2GUESS/man/R2GUESS.Rd R2GUESS/man/Analysis.permutation.Rd R2GUESS/man/Extend.R2GUESS.Rd R2GUESS/man/Postprocess.R2GUESS.Rd R2GUESS/man/data.X.Rd R2GUESS/man/summary.ESS.Rd R2GUESS/man/print.ESS.Rd R2GUESS/man/wrapper.Rd R2GUESS/man/sample.beta.Rd R2GUESS/man/example.as.ESS.object.Rd R2GUESS/man/MAP.file.Rd R2GUESS/man/Resume.R2GUESS.Rd R2GUESS/man/plotcim.Rd R2GUESS/man/data.Y.Hopx.Rd R2GUESS/man/boxplotbeta.Rd R2GUESS/man/R2GUESS-package.Rd R2GUESS/man/plotMPPI.Rd R2GUESS/man/plotmodel.Rd R2GUESS/man/FDR.permutation.Rd R2GUESS/man/as.ESS.object.Rd R2GUESS/man/get.sweep.best.model.Rd R2GUESS/man/get.g.sweep.Rd
R2GUESS/cleanup
R2GUESS/tools
R2GUESS/tools/gsl.m4
R2GUESS/tools/cula.m4

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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