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The package can also use robust regression (unpublished work) and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 |
Documentation:
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