BayesSUR v1.1-2

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Bayesian Seemingly Unrelated Regression

Bayesian seemingly unrelated regression with general variable selection and dense/sparse covariance matrix. The sparse seemingly unrelated regression is described in Banterle et al. (2018) <doi:10.1101/467019>.

Functions in BayesSUR

Name Description
coef.BayesSUR extract the posterior mean of the coefficients of a "BayesSUR" class object
plot.CPO plot the conditional predictive ordinate
example_GDSC Preprocessed data set to mimic a small pharmacogenetic example
fitted.BayesSUR fitted response values corresponds to the posterior mean estimates
elpd measure the prediction accuracy by the expected log pointwise predictive density
plot.Estimator plot the posterior mean estimators
plot.Network plot the network representation of the associations between responses and predictors
plot.Manhattan plot Manhattan-like plots for marginal posterior inclusion probabilities (mPIP) and numbers of responses of association for predictors
plot.MCMCdiag show trace plots and diagnostic density plots
print.BayesSUR print a short summary of the Bayesian Seemingly Unrelated Regressions Fits
summary.BayesSUR summarizing Bayesian Seemingly Unrelated Regressions Fits
targetGene targetGene
predict.BayesSUR predict responses corresponding to the posterior mean of the coefficients, return posterior mean of coefficients or indices of nonzero coefficients
plot.ResponseGraph plot the estimated graph for multiple response variables
BayesSUR_internal BayesSUR_internal
getEstimator extract the posterior mean of the parameters
BayesSUR main function of the package
example_eQTL Simulated data set to mimic a small expression quantitative trait loci (eQTL) example
plot.BayesSUR create a selection of plots for a "BayesSUR" class object
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Vignettes of BayesSUR

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BayesSUR.pdf.asis
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Details

Type Package
Date 2020-04-25
License MIT + file LICENSE
Copyright The C++ files pugixml.cpp, pugixml.hpp and pugiconfig.hpp are Copyright (C) 2006-2018 by Arseny Kapoulkine (arseny.kapoulkine@gmail.com) and Copyright (C) 2003 by Kristen Wegner (kristen@tima.net). The R function vertical.image.legend() has Copyright (C) 2013 by Jenise Swall (jswall@vcu.edu).
VignetteBuilder R.rsp
RoxygenNote 7.1.0
Encoding UTF-8
LinkingTo Rcpp, RcppArmadillo (>= 0.9.000)
LazyData true
NeedsCompilation yes
SystemRequirements C++11
Packaged 2020-04-25 15:43:23 UTC; zhiz
Repository CRAN
Date/Publication 2020-04-27 14:00:18 UTC

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