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gcatest

This is the development version of gcatest; for the stable release version, see gcatest.

Genotype Conditional Association TEST


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews DimensionReduction, GenomeWideAssociation, PrincipalComponent, SNP, Software
Version 2.3.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 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
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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_2.3.0.tar.gz
Windows Binary gcatest_2.3.0.zip (64-bit only)
macOS Binary (x86_64) gcatest_2.3.0.tgz
macOS Binary (arm64)
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