Package: GMMAT 1.4.2

GMMAT: Generalized Linear Mixed Model Association Tests

Perform association tests using generalized linear mixed models (GLMMs) in genome-wide association studies (GWAS) and sequencing association studies. First, GMMAT fits a GLMM with covariate adjustment and random effects to account for population structure and familial or cryptic relatedness. For GWAS, GMMAT performs score tests for each genetic variant as proposed in Chen et al. (2016) <doi:10.1016/j.ajhg.2016.02.012>. For candidate gene studies, GMMAT can also perform Wald tests to get the effect size estimate for each genetic variant. For rare variant analysis from sequencing association studies, GMMAT performs the variant Set Mixed Model Association Tests (SMMAT) as proposed in Chen et al. (2019) <doi:10.1016/j.ajhg.2018.12.012>, including the burden test, the sequence kernel association test (SKAT), SKAT-O and an efficient hybrid test of the burden test and SKAT, based on user-defined variant sets.

Authors:Han Chen [aut, cre], Matthew Conomos [aut], Duy Pham [aut], Arthor Gilly [ctb], Robert Gentleman [ctb, cph], Ross Ihaka [ctb, cph], The R Core Team [ctb, cph], The R Foundation [cph], Eric Biggers [ctb, cph], Tino Reichardt [ctb, cph], Meta Platforms, Inc. and affiliates [cph]

GMMAT_1.4.2.tar.gz
GMMAT_1.4.2.zip(r-4.5)GMMAT_1.4.2.zip(r-4.4)GMMAT_1.4.2.zip(r-4.3)
GMMAT_1.4.2.tgz(r-4.4-x86_64)GMMAT_1.4.2.tgz(r-4.4-arm64)GMMAT_1.4.2.tgz(r-4.3-x86_64)GMMAT_1.4.2.tgz(r-4.3-arm64)
GMMAT_1.4.2.tar.gz(r-4.5-noble)GMMAT_1.4.2.tar.gz(r-4.4-noble)
GMMAT_1.4.2.tgz(r-4.4-emscripten)GMMAT_1.4.2.tgz(r-4.3-emscripten)
GMMAT.pdf |GMMAT.html✨
GMMAT/json (API)

# Install 'GMMAT' in R:
install.packages('GMMAT', repos = c('https://hanchenphd.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/hanchenphd/gmmat/issues

Uses libs:
  • openblas– Optimized BLAS
  • zlib– Compression library
  • bzip2– High-quality block-sorting file compressor library
  • libzstd– Fast lossless compression algorithm
  • libdeflate– Fast, whole-buffer DEFLATE-based compression and decompression
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

8 exports 36 stars 4.48 score 9 dependencies 2 dependents 26 mentions 89 scripts 518 downloads

Last updated 10 months agofrom:850cb068c3. Checks:ERROR: 2 OK: 4 NOTE: 3. Indexed: yes.

TargetResultDate
Doc / VignettesFAILAug 27 2024
R-4.5-win-x86_64NOTEAug 27 2024
R-4.5-linux-x86_64ERRORAug 27 2024
R-4.4-win-x86_64NOTEAug 27 2024
R-4.4-mac-x86_64OKAug 27 2024
R-4.4-mac-aarch64OKAug 27 2024
R-4.3-win-x86_64NOTEAug 27 2024
R-4.3-mac-x86_64OKAug 27 2024
R-4.3-mac-aarch64OKAug 27 2024

Exports:glmm.scoreglmm.score.metaglmm.waldglmmkinSMMATSMMAT.lowmemSMMAT.metaSMMAT.prep

Dependencies:codetoolsCompQuadFormdata.tableforeachiteratorslatticeMatrixRcppRcppArmadillo

GMMAT

Rendered fromGMMAT.Rnwusingutils::Sweaveon Aug 27 2024.

Last update: 2023-11-17
Started: 2018-03-31