Package: gcatest 2.13.0

Alejandro Ochoa

gcatest: Genotype Conditional Association TEST

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.

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

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manual.pdf |manual.html✨
card.svg |card.png
gcatest/json (API)
NEWS

# Install 'gcatest' in R:

install.packages('gcatest', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/storeylab/gcatest/issues

Datasets:

sim_geno - Simulated data from PSD model
sim_trait - Simulated data from PSD model

On BioConductor:gcatest-2.13.0(bioc 3.24)gcatest-2.12.0(bioc 3.23)

snp dimensionreduction principalcomponent genomewideassociation

5.43 score 6 stars 5 scripts 345 downloads 4 exports 36 dependencies

Last updated from:d5181b61f0. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	153
linux-devel-x86_64	OK	232
source / vignettes	OK	196
linux-release-x86_64	OK	190
macos-release-arm64	OK	113
macos-oldrel-arm64	OK	86
windows-devel	OK	104
windows-release	OK	139
windows-oldrel	OK	121
wasm-release	OK	130

Exports:delta_deviance_lf gcat gcat.stat gcatest

Dependencies:BEDMatrix bit bit64 cli clipr corpcor cpp11 crayon crochet dplyr generics genio glue hms lattice lfa lifecycle magrittr Matrix pillar pkgconfig prettyunits progress R6 Rcpp RcppEigen readr rlang RSpectra tibble tidyselect tzdb utf8 vctrs vroom withr

Genotype Conditional Association Test Vignette

Wei Hao, Minsun Song, Alejandro Ochoa, John D. Storey

Rendered fromgcatest.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2026-01-28
Started: 2026-01-28

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate delta deviance of logistic null/alternative models	delta_deviance_lf
Genotype Conditional Association TEST	gcat gcat.stat gcatest
Simulated data from PSD model	sim_geno
Simulated data from PSD model	sim_trait