MiRKAT: Microbiome Regression-Based Kernel Association Tests

Test for overall association between microbiome composition data and phenotypes via phylogenetic kernels. The phenotype can be univariate continuous or binary (Zhao et al. (2015) <doi:10.1016/j.ajhg.2015.04.003>), survival outcomes (Plantinga et al. (2017) <doi:10.1186/s40168-017-0239-9>), multivariate (Zhan et al. (2017) <doi:10.1002/gepi.22030>) and structured phenotypes (Zhan et al. (2017) <doi:10.1111/biom.12684>). The package can also use robust regression (unpublished work) and integrated quantile regression (Wang et al. (2021) <doi:10.1093/bioinformatics/btab668>). In each case, the microbiome community effect is modeled nonparametrically through a kernel function, which can incorporate phylogenetic tree information.

Version: 1.2.3
Depends: R (≥ 3.1.0)
Imports: MASS, CompQuadForm, quantreg, GUniFrac, PearsonDS, lme4, Matrix, permute, mixtools, survival, stats
Suggests: knitr, vegan, rmarkdown, magrittr, kableExtra
Published: 2023-02-17
DOI: 10.32614/CRAN.package.MiRKAT
Author: Anna Plantinga [aut, cre], Nehemiah Wilson [aut, ctb], Haotian Zheng [aut, ctb], Tianying Wang [aut, ctb], Xiang Zhan [aut, ctb], Michael Wu [aut], Ni Zhao [aut, ctb], Jun Chen [aut]
Maintainer: Anna Plantinga <amp9 at williams.edu>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: no
CRAN checks: MiRKAT results


Reference manual: MiRKAT.pdf
Vignettes: MiRKAT Package Vignette


Package source: MiRKAT_1.2.3.tar.gz
Windows binaries: r-devel: MiRKAT_1.2.3.zip, r-release: MiRKAT_1.2.3.zip, r-oldrel: MiRKAT_1.2.3.zip
macOS binaries: r-release (arm64): MiRKAT_1.2.3.tgz, r-oldrel (arm64): MiRKAT_1.2.3.tgz, r-release (x86_64): MiRKAT_1.2.3.tgz, r-oldrel (x86_64): MiRKAT_1.2.3.tgz
Old sources: MiRKAT archive


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