R2GUESS: Wrapper Functions for GUESS

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

Author
Gianluca Campanella [cre], Benoit Liquet [aut], Marc Chadeau-Hyam [aut], Leonardo Bottolo [ctb], Sylvia Richardson [ctb]
Date of publication
2016-01-26 15:19:28
Maintainer
Gianluca Campanella <gianluca@campanella.org>
License
GPL (>= 2)
Version
1.7

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