gcatest

This is the released version of gcatest; for the devel version, see gcatest.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2

Genotype Conditional Association TEST

Bioconductor version: Release (3.23)

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] ORCID: 0000-0003-4928-3403 , John D. Storey [aut] ORCID: 0000-0001-5992-402X

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

Citation (from within R, enter citation("gcatest")):

Wei Hao, Minsun Song, Alejandro Ochoa, John D. Storey. gcatest: Genotype Conditional Association TEST. doi:10.18129/B9.bioc.gcatest, R package version 2.12.0, https://bioconductor.org/packages/gcatest.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

gcatest Package	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DimensionReduction, GenomeWideAssociation, PrincipalComponent, SNP, Software
Version	2.12.0
In Bioconductor since	BioC 3.2 (R-3.2) (11 years)
License	GPL (>= 3)
Depends	R (>= 4.0)
Imports	methods, lfa
System Requirements
URL	https://github.com/StoreyLab/gcatest
Bug Reports	https://github.com/StoreyLab/gcatest/issues

Suggests	knitr, rmarkdown, ggplot2, testthat, BEDMatrix, genio
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	jackstraw
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	gcatest_2.12.0.tar.gz
Windows Binary (x86_64)	gcatest_2.12.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	gcatest_2.12.0.tgz
macOS Binary (sonoma-arm64)	gcatest_2.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/gcatest
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/gcatest
Package Short Url	https://bioconductor.org/packages/gcatest/
Package Downloads Report	Download Stats