GGPA

DOI: 10.18129/B9.bioc.GGPA  

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

Bioconductor version: Release (3.17)

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.

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

Maintainer: Dongjun Chung <dongjun.chung at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GGPA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GGPA")

 

PDF	R Script	GGPA
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, Clustering, DifferentialExpression, GeneExpression, Genetics, GenomeWideAssociation, MultipleComparison, Preprocessing, SNP, Software, StatisticalMethod
Version	1.12.1
In Bioconductor since	BioC 3.11 (R-4.0) (3.5 years)
License	GPL (>= 2)
Depends	R (>= 4.0.0), stats, methods, graphics, GGally, network, sna, scales, matrixStats
Imports	Rcpp (>= 0.11.3)
LinkingTo	Rcpp, RcppArmadillo
Suggests	BiocStyle
SystemRequirements	GNU make
Enhances
URL	https://github.com/dongjunchung/GGPA/
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	GGPA_1.12.1.tar.gz
Windows Binary	GGPA_1.12.1.zip
macOS Binary (x86_64)	GGPA_1.12.1.tgz
macOS Binary (arm64)	GGPA_1.12.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GGPA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GGPA
Bioc Package Browser	https://code.bioconductor.org/browse/GGPA/
Package Short Url	https://bioconductor.org/packages/GGPA/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive