Package: varbvs 2.6-10

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.

Authors:Peter Carbonetto [aut, cre], Matthew Stephens [aut], David Gerard [ctb]

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varbvs.pdf |varbvs.html
varbvs/json (API)

# Install 'varbvs' in R:
install.packages('varbvs', repos = c('https://pcarbo.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/pcarbo/varbvs/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • cytokine - Cytokine signaling genes SNP annotation.
  • leukemia - Expression levels recorded in leukemia patients.

On CRAN:

4.83 score 2 packages 142 scripts 287 downloads 2 mentions 34 exports 12 dependencies

Last updated 1 years agofrom:547e829ff3. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 13 2024
R-4.5-win-x86_64OKNov 13 2024
R-4.5-linux-x86_64OKNov 13 2024
R-4.4-win-x86_64OKNov 13 2024
R-4.4-mac-x86_64OKNov 13 2024
R-4.4-mac-aarch64OKNov 13 2024
R-4.3-win-x86_64OKNov 13 2024
R-4.3-mac-x86_64OKNov 13 2024
R-4.3-mac-aarch64OKNov 13 2024

Exports:bayesfactorcase.names.varbvscoef.varbvscoef.varbvsmixconfint.varbvscreddeviance.varbvsfitted.varbvslabels.varbvsnobs.varbvsnormalizelogweightsplot.varbvspredict.varbvspredict.varbvsmixprint.summary.varbvsprint.varbvsrandrandnresid.varbvsresiduals.varbvssubset.varbvssummary.varbvsvar1var1.colsvarbvsvarbvsbfvarbvsbinvarbvsbinzvarbvsindepvarbvsmixvarbvsnormvarbvsproxybfvarbvspvevariable.names.varbvs

Dependencies:deldirinterpjpeglatticelatticeExtraMASSMatrixnor1mixpngRColorBrewerRcppRcppEigen

Mapping disease risk loci using varbvs

Rendered fromcd.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2017-09-08
Started: 2017-03-24

Assessing support for gene sets in disease using varbvs

Rendered fromcytokine.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2017-09-08
Started: 2017-03-24

Mapping QTLs in outbred mice using varbvs

Rendered fromcfw.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2019-03-07
Started: 2017-03-24

Comparison of glmnet and varbvs in Leukemia data set

Rendered fromleukemia.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2019-03-07
Started: 2017-03-24