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.

Install the latest version of this package by entering the following in R:
install.packages("varbvs")
AuthorPeter Carbonetto, Matthew Stephens, David Gerard
Date of publication2017-03-24 05:37:09 UTC
MaintainerPeter Carbonetto <peter.carbonetto@gmail.com>
LicenseGPL (>= 3)
Version2.0-8
http://github.com/pcarbo/varbvs

View on CRAN

Functions

bayesfactor Man page
cred Man page
cytokine Man page
diagsq Man page
diagsqt Man page
leukemia Man page
logit Man page
logpexp Man page
logsigmoid Man page
normalizelogweights Man page
plot.varbvs Man page
predict.varbvs Man page
print.summary.varbvs Man page
rand Man page
randn Man page
sigmoid Man page
subset.varbvs Man page
summary.varbvs Man page
update_eta Man page
update_etaz Man page
updatestats_varbvsbin Man page
updatestats_varbvsbinz Man page
var1 Man page
var1.cols Man page
varbvs Man page
varbvsbin Man page
varbvsbinupdate Man page
varbvsbinz Man page
varbvsbinzupdate Man page
varbvscoefcred Man page
varbvsindep Man page
varbvsnorm Man page
varbvsnormupdate Man page
varbvs-package Man page
varbvspve Man page

Files

inst
inst/CITATION
inst/doc
inst/doc/cfw.Rmd
inst/doc/leukemia.R
inst/doc/cfw.html
inst/doc/cfw.R inst/doc/cytokine.R
inst/doc/cytokine.html
inst/doc/cytokine.Rmd
inst/doc/leukemia.Rmd
inst/doc/cd.Rmd
inst/doc/cd.html
inst/doc/leukemia.html
inst/doc/cd.R
tests
tests/testthat.R
tests/testthat
tests/testthat/demo.cc.R tests/testthat/test_varbvs.R tests/testthat/demo.qtl.R tests/testthat/test_varbvsnormupdate.R
src
src/diagsq.h
src/misc.c
src/varbvs.h
src/varbvsr.h
src/misc.h
src/varbvsr.c
src/diagsqr.c
src/types.h
src/varbvs.c
src/init.c
src/RcppExports.cpp
src/varbvsnormupdate_rcpp.cpp
src/diagsq.c
NAMESPACE
data
data/cytokine.RData
data/datalist
data/leukemia.RData
R
R/varbvsbinz.R R/varbvsnormupdate.R R/bayesfactor.R R/subset.varbvs.R R/varbvscoefcred.R R/varbvsbinzupdate.R R/predict.varbvs.R R/varbvspve.R R/varbvsindep.R R/varbvsbin.R R/varbvs.R R/RcppExports.R R/summary.varbvs.R R/varbvsbinupdate.R R/varbvsnorm.R R/plot.varbvs.R R/misc.R
vignettes
vignettes/cfw.Rmd
vignettes/cytokine.Rmd
vignettes/leukemia.Rmd
vignettes/cd.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/varbvs-package.Rd man/varbvscoefcred.Rd man/varbvs-internal.Rd man/leukemia.Rd man/rand.Rd man/varbvsindep.Rd man/plot.varbvs.Rd man/bayesfactor.Rd man/normalizelogweights.Rd man/varbvs.Rd man/cred.Rd man/predict.varbvs.Rd man/subset.varbvs.Rd man/cytokine.Rd man/summary.varbvs.Rd

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.