Package: GGPA 1.25.0

Dongjun Chung

GGPA: graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture

Genome-wide association studies (GWAS) is a widely used tool for identification of genetic variants associated with phenotypes and diseases, though complex diseases featuring many genetic variants with small effects present difficulties for traditional these studies. By leveraging pleiotropy, the statistical power of a single GWAS can be increased. This package provides functions for fitting graph-GPA, a statistical framework to prioritize GWAS results by integrating pleiotropy. 'GGPA' package provides user-friendly interface to fit graph-GPA models, implement association mapping, and generate a phenotype graph.

Authors:Dongjun Chung, Hang J. Kim, Carter Allen

GGPA_1.25.0.tar.gz
GGPA_1.25.0.zip(r-4.7)GGPA_1.25.0.zip(r-4.6)GGPA_1.25.0.zip(r-4.5)
GGPA_1.25.0.tgz(r-4.6-x86_64)GGPA_1.25.0.tgz(r-4.6-arm64)GGPA_1.25.0.tgz(r-4.5-x86_64)GGPA_1.25.0.tgz(r-4.5-arm64)
GGPA_1.25.0.tar.gz(r-4.7-arm64)GGPA_1.25.0.tar.gz(r-4.7-x86_64)GGPA_1.25.0.tar.gz(r-4.6-arm64)GGPA_1.25.0.tar.gz(r-4.6-x86_64)
GGPA_1.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
GGPA/json (API)
NEWS

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

Bug tracker:https://github.com/dongjunchung/ggpa/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:GGPA-1.25.0(bioc 3.24)GGPA-1.24.0(bioc 3.23)

softwarestatisticalmethodclassificationgenomewideassociationsnpgeneticsclusteringmultiplecomparisonpreprocessinggeneexpressiondifferentialexpressionopenblascpp

4.00 score 1 stars 6 scripts 321 downloads 6 exports 46 dependencies

Last updated from:9f0cd11566. Checks:1 ERROR, 7 NOTE, 2 OK, 4 WARNING. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR167
linux-devel-arm64NOTE256
linux-devel-x86_64NOTE317
source / vignettesOK240
linux-release-arm64NOTE248
linux-release-x86_64NOTE315
macos-release-arm64WARNING218
macos-release-x86_64WARNING319
macos-oldrel-arm64WARNING183
macos-oldrel-x86_64WARNING350
windows-develNOTE327
windows-releaseNOTE337
windows-oldrelNOTE360
wasm-releaseOK132

Exports:assocestimatesfdrGGPAplotshow

Dependencies:clicodacpp11crayondplyrfarverforcatsgenericsGGallyggplot2ggstatsgluegtablehmsisobandlabelinglatticelifecyclemagrittrMatrixmatrixStatsnetworkpatchworkpillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppRcppArmadillorlangS7scalessnastatnet.commonstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

GGPA

Rendered fromGGPA-example.Rnwusingutils::Sweaveon May 30 2026.

Last update: 2020-04-12
Started: 2020-02-25

Readme and manuals

Help Manual

Help pageTopics
graph-GPAGGPA-package
Association mappingassoc assoc,GGPA-method
Fit graph-GPA modelGGPA
Class "GGPA"estimates estimates,GGPA-method fdr fdr,GGPA-method GGPA-class plot,GGPA,missing-method plot,GGPA-method show,GGPA-method
Simulation dataa for graph-GPAsimulation