Package: MiSPU 1.0
MiSPU: Microbiome Based Sum of Powered Score (MiSPU) Tests
There is an increasing interest in investigating how the compositions of microbial communities are associated with human health and disease. In this package, we present a novel global testing method called aMiSPU, that is highly adaptive and thus high powered across various scenarios, alleviating the issue with the choice of a phylogenetic distance. Our simulations and real data analysis demonstrated that aMiSPU test was often more powerful than several competing methods while correctly controlling type I error rates.
Authors:
MiSPU_1.0.tar.gz
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MiSPU.pdf |MiSPU.html✨
MiSPU/json (API)
| # Install 'MiSPU' in R: |
| install.packages('MiSPU', repos = c('https://chongwu-biostat.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/chongwu-biostat/mispu/issues
- dd - The estimate of Dirichlet-multinomial distribution
- throat.meta - Meta data of the throat microbiome samples.
- throat.otu.tab - OTU count table from 16S sequencing of the throat microbiome samples.
- throat.tree - UPGMA tree of the OTUs from 16S sequencing of the throat microbiome samples.
Last updated 7 years agofrom:baeb8678fa. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 10 2024 |
| R-4.5-win-x86_64 | NOTE | Nov 10 2024 |
| R-4.5-linux-x86_64 | NOTE | Nov 10 2024 |
| R-4.4-win-x86_64 | NOTE | Nov 10 2024 |
| R-4.4-mac-x86_64 | NOTE | Nov 10 2024 |
| R-4.4-mac-aarch64 | NOTE | Nov 10 2024 |
| R-4.3-win-x86_64 | NOTE | Nov 10 2024 |
| R-4.3-mac-x86_64 | NOTE | Nov 10 2024 |
| R-4.3-mac-aarch64 | NOTE | Nov 10 2024 |
Exports:correspLeavesGUniFracMiSPUrankingrdirichletsimulateData
Dependencies:apeaSPUclusterdigestdotCall64fieldsgeelatticemapsMASSMatrixmatrixStatsmgcvmvtnormnlmepermuteRcppRcppArmadillospamveganviridisLite
