gcatest

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see gcatest.

Genotype Conditional Association TEST

Bioconductor version: 3.21

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

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

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

Installation

To install this package, start R (version "4.5") 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")

gcat Package PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DimensionReduction, GenomeWideAssociation, PrincipalComponent, SNP, Software

Version 2.8.0

In Bioconductor since BioC 3.2 (R-3.2) (10 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, ggplot2, testthat, BEDMatrix, genio

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Package Archives

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

Source Package gcatest_2.8.0.tar.gz

Windows Binary (x86_64) gcatest_2.8.0.zip

macOS Binary (x86_64) gcatest_2.8.0.tgz

macOS Binary (arm64) gcatest_2.8.0.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/

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