gcatest

DOI: 10.18129/B9.bioc.gcatest  

Genotype Conditional Association TEST

Bioconductor version: Release (3.17)

GCAT is an association test for genome wide association studies that controls for population structure under a general class of trait models. This test conditions on the trait, which makes it immune to confounding by unmodeled environmental factors. Population structure is modeled via logistic factors, which are estimated using the `lfa` package.

Author: Wei Hao [aut], Minsun Song [aut], Alejandro Ochoa [aut, cre] , John D. Storey [aut]

Maintainer: Alejandro Ochoa <alejandro.ochoa at duke.edu>

Installation

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

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

BiocManager::install("gcatest")

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("gcatest")

 

PDF	R Script	gcat Package
PDF		Reference Manual
Text		NEWS

Details

biocViews	DimensionReduction, GenomeWideAssociation, PrincipalComponent, SNP, Software
Version	2.0.7
In Bioconductor since	BioC 3.2 (R-3.2) (8 years)
License	GPL (>= 3)
Depends	R (>= 4.0)
Imports	methods, lfa
LinkingTo
Suggests	knitr, ggplot2, testthat, BEDMatrix, genio
SystemRequirements
Enhances
URL	https://github.com/StoreyLab/gcatest
BugReports	https://github.com/StoreyLab/gcatest/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	gcatest_2.0.7.tar.gz
Windows Binary	gcatest_2.0.7.zip
macOS Binary (x86_64)	gcatest_2.0.7.tgz
macOS Binary (arm64)	gcatest_2.0.7.tgz
Source Repository	git clone https://git.bioconductor.org/packages/gcatest
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/gcatest
Bioc Package Browser	https://code.bioconductor.org/browse/gcatest/
Package Short Url	https://bioconductor.org/packages/gcatest/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive