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✨
DESCRIPTION |NEWS
card.svg |card.png
GGPA/json (API)

# 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:

simulation - Simulation dataa for graph-GPA

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

software statisticalmethod classification genomewideassociation snp genetics clustering multiplecomparison preprocessing geneexpression differentialexpression openblas cpp

4.00 score 1 stars 2 scripts 6 exports 46 dependencies

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

Target	Result	Time
bioc-checks	ERROR	179
linux-devel-arm64	NOTE	248
linux-devel-x86_64	NOTE	297
source / vignettes	OK	258
linux-release-arm64	NOTE	245
linux-release-x86_64	NOTE	302
macos-release-arm64	WARNING	212
macos-release-x86_64	WARNING	477
macos-oldrel-arm64	WARNING	214
macos-oldrel-x86_64	WARNING	335
windows-devel	NOTE	355
windows-release	NOTE	355
windows-oldrel	NOTE	302
wasm-release	OK	175

Exports:assoc estimates fdr GGPA plot show

Dependencies:cli coda cpp11 crayon dplyr farver forcats generics GGally ggplot2 ggstats glue gtable hms isoband labeling lattice lifecycle magrittr Matrix matrixStats network patchwork pillar pkgconfig prettyunits progress purrr R6 RColorBrewer Rcpp RcppArmadillo rlang S7 scales sna statnet.common stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr

GGPA

Overview | Workflow | Investigation of Pleiotropic Architecture Using the Phenotype Graph | graph-GPA Analysis Using a Prior Disease Graph

Rendered fromGGPA-example.Rnwusingutils::Sweave

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

Help page	Topics
graph-GPA	GGPA-package
Association mapping	assoc assoc,GGPA-method
Fit graph-GPA model	GGPA
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-GPA	simulation

Package: GGPA 1.25.0

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

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)