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 The package can also use robust regression (unpublished work) and integrated quantile regression (Wang et al.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.html , MiRKAT.pdf |
| Vignettes: |
MiRKAT Package Vignette (source, R code) |
| 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 |
| Reverse imports: | ROKET |
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