varbvs: Large-Scale Bayesian Variable Selection Using Variational Methods

Fast algorithms for fitting Bayesian variable selection models and computing Bayes factors, in which the outcome (or response variable) is modeled using a linear regression or a logistic regression. The algorithms are based on the variational approximations described in "Scalable variational inference for Bayesian variable selection in regression, and its accuracy in genetic association studies" (P. Carbonetto & M. Stephens, 2012, <DOI:10.1214/12-BA703>). This software has been applied to large data sets with over a million variables and thousands of samples.

Author
Peter Carbonetto, Matthew Stephens
Date of publication
2016-05-28 17:52:03
Maintainer
Peter Carbonetto <peter.carbonetto@gmail.com>
License
GPL (>= 3)
Version
2.0.0
URLs

View on CRAN

Man pages

bayesfactor
Compute numerical estimate of Bayes factor.
cred
Estimate credible interval.
cytokine
Cytokine signaling genes SNP annotation.
leukemia
Expression levels recorded in leukemia patients.
normalizelogweights
Compute normalized probabilities.
plot.varbvs
Summarize variable selection results in a single plot.
predict.varbvs
Make predictions from a model fitted by varbvs.
rand
Return matrices of pseudorandom values.
summary.varbvs
Summarize a fitted variable selection model.
varbvs
Fit variable selection model using variational approximation...
varbvscoefcred
Compute credible intervals for regression coefficients.
varbvsindep
Compute posterior statistics, ignoring correlations.
varbvs-internal
Internal varbvs functions
varbvs-package
Large-scale Bayesian variable selection using variational...

Files in this package

varbvs
varbvs/inst
varbvs/inst/CITATION
varbvs/src
varbvs/src/diagsq.h
varbvs/src/misc.c
varbvs/src/varbvs.h
varbvs/src/misc.h
varbvs/src/varbvsr.c
varbvs/src/diagsqr.c
varbvs/src/types.h
varbvs/src/varbvs.c
varbvs/src/diagsq.c
varbvs/NAMESPACE
varbvs/data
varbvs/data/cytokine.RData
varbvs/data/datalist
varbvs/data/leukemia.RData
varbvs/R
varbvs/R/varbvsbinz.R
varbvs/R/varbvsnormupdate.R
varbvs/R/bayesfactor.R
varbvs/R/varbvscoefcred.R
varbvs/R/varbvsbinzupdate.R
varbvs/R/predict.varbvs.R
varbvs/R/varbvspve.R
varbvs/R/varbvsindep.R
varbvs/R/varbvsbin.R
varbvs/R/varbvs.R
varbvs/R/summary.varbvs.R
varbvs/R/varbvsbinupdate.R
varbvs/R/varbvsnorm.R
varbvs/R/plot.varbvs.R
varbvs/R/misc.R
varbvs/vignettes
varbvs/vignettes/demo.cc.R
varbvs/vignettes/demo.cytokine.R
varbvs/vignettes/demo.cfw.R
varbvs/vignettes/demo.qtl.R
varbvs/vignettes/demo.leukemia.R
varbvs/vignettes/demo.cd.R
varbvs/MD5
varbvs/DESCRIPTION
varbvs/man
varbvs/man/varbvs-package.Rd
varbvs/man/varbvscoefcred.Rd
varbvs/man/varbvs-internal.Rd
varbvs/man/leukemia.Rd
varbvs/man/rand.Rd
varbvs/man/varbvsindep.Rd
varbvs/man/plot.varbvs.Rd
varbvs/man/bayesfactor.Rd
varbvs/man/normalizelogweights.Rd
varbvs/man/varbvs.Rd
varbvs/man/cred.Rd
varbvs/man/predict.varbvs.Rd
varbvs/man/cytokine.Rd
varbvs/man/summary.varbvs.Rd