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...

Functions

Analysis.permutation Man page
as.ESS.object Man page
boxplotbeta Man page
check.convergence Man page
data.X Man page
data.Y.Hopx Man page
example.as.ESS.object Man page
Extend.R2GUESS Man page
FDR.permutation Man page
get.best.models Man page
get.g.sweep Man page
get.sweep.best.model Man page
MAP.file Man page
pairwise.correlation Man page
plotcim Man page
plotcim.explore Man page
plot.ESS Man page
plotmodel Man page
plotMPPI Man page
plotvariable Man page
Postprocess.R2GUESS Man page
print.ESS Man page
R2GUESS Man page
R2GUESS-package Man page
R2GUESS.perm Man page
Resume.R2GUESS Man page
sample.beta Man page
summarybest.model Man page
summary.ESS Man page
wrapper Man page

Files

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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