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Genotype Conditional Association TEST

Bioconductor version: Release (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>

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


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

if (!require("BiocManager", quietly = TRUE))


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


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

gcat Package PDF R Script
Reference Manual PDF


biocViews DimensionReduction, GenomeWideAssociation, PrincipalComponent, SNP, Software
Version 2.4.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License GPL (>= 3)
Depends R (>= 4.0)
Imports methods, lfa
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Suggests knitr, ggplot2, testthat, BEDMatrix, genio
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Follow Installation instructions to use this package in your R session.

Source Package gcatest_2.4.0.tar.gz
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macOS Binary (x86_64) gcatest_2.4.0.tgz
macOS Binary (arm64) gcatest_2.4.0.tgz
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