Package: CPBayes 1.1.0

CPBayes: Bayesian Meta Analysis for Studying Cross-Phenotype Genetic Associations

A Bayesian meta-analysis method for studying cross-phenotype genetic associations. It uses summary-level data across multiple phenotypes to simultaneously measure the evidence of aggregate-level pleiotropic association and estimate an optimal subset of traits associated with the risk locus. CPBayes is based on a spike and slab prior. The methodology is available from: A Majumdar, T Haldar, S Bhattacharya, JS Witte (2018) <doi:10.1371/journal.pgen.1007139>.

Authors:Arunabha Majumdar <[email protected]> [aut, cre], Tanushree Haldar <[email protected]> [aut], John Witte [ctb]

CPBayes_1.1.0.tar.gz
CPBayes_1.1.0.zip(r-4.7)CPBayes_1.1.0.zip(r-4.6)CPBayes_1.1.0.zip(r-4.5)
CPBayes_1.1.0.tgz(r-4.6-any)CPBayes_1.1.0.tgz(r-4.5-any)
CPBayes_1.1.0.tar.gz(r-4.7-any)CPBayes_1.1.0.tar.gz(r-4.6-any)
CPBayes_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CPBayes/json (API)

# Install 'CPBayes' in R:

install.packages('CPBayes', repos = c('https://arunabhacodes.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/arunabhacodes/cpbayes/issues

Datasets:

ExampleDataCor - An example data for correlated summary statistics.
ExampleDataUncor - An example data for uncorrelated summary statistics.
SampleOverlapMatrix - An example data of sample-overlap matrices.

On CRAN:

4.26 score 3 stars 12 scripts 332 downloads 1 mentions 7 exports 13 dependencies

Last updated from:4df15cb9d3. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	142
source / vignettes	OK	206
linux-release-x86_64	OK	136
macos-release-arm64	OK	203
macos-oldrel-arm64	OK	159
windows-devel	OK	85
windows-release	OK	88
windows-oldrel	OK	82
wasm-release	OK	109

Exports:analytic_locFDR_BF_cor analytic_locFDR_BF_uncor cpbayes_cor cpbayes_uncor estimate_corln forest_cpbayes post_summaries

Dependencies:abind backports checkmate cli forestplot glue lifecycle magrittr MASS mvtnorm purrr rlang vctrs

CPBayes (Bayesian meta analysis for studying cross-phenotype genetic associations) package

Introduction | Installation | How to run CPBayes for uncorrelated summary statistics. | How to run CPBayes for correlated summary statistics. | How to run estimate_corln.

Rendered fromcpbayes.Rmdusingknitr::rmarkdown

Last update: 2020-12-01
Started: 2017-01-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Analytic calculation of the local FDR & Bayes factor for correlated summary statistics.	analytic_locFDR_BF_cor
Analytic calculation of the local FDR & Bayes factor for uncorrelated summary statistics.	analytic_locFDR_BF_uncor
CPBayes: An R-package implemeting a Bayesian meta analysis method for studying cross-phenotype genetic associations.	CPBayes
Run correlated version of CPBayes.	cpbayes_cor
Run uncorrelated version of CPBayes.	cpbayes_uncor
Estimate correlation structure of beta-hat vector for multiple overlapping case-control studies using sample-overlap matrices.	estimate_corln
An example data for correlated summary statistics.	ExampleDataCor
An example data for uncorrelated summary statistics.	ExampleDataUncor
Forest plot presenting pleiotropy result obtained by CPBayes.	forest_cpbayes
Post summary of the MCMC data generated by the uncorrelated or correlated version of CPBayes.	post_summaries
An example data of sample-overlap matrices.	SampleOverlapMatrix