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https://github.com/Zhiwen-Owen-Jiang/MiRKATMC
The Microbiome Regression-based Kernel Association Test for multi-categorical (nominal or ordinal) data
https://github.com/Zhiwen-Owen-Jiang/MiRKATMC
Last synced: 11 days ago
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The Microbiome Regression-based Kernel Association Test for multi-categorical (nominal or ordinal) data
- Host: GitHub
- URL: https://github.com/Zhiwen-Owen-Jiang/MiRKATMC
- Owner: Zhiwen-Owen-Jiang
- License: gpl-3.0
- Created: 2021-01-11T17:12:37.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2023-04-15T01:52:11.000Z (over 1 year ago)
- Last Synced: 2024-08-01T16:18:38.551Z (3 months ago)
- Language: R
- Size: 55.7 KB
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
Awesome Lists containing this project
- awesome-rm-omics - **MiRKAT-MC** - Jiang - [MiRKAT-MC: A Distance-Based Microbiome Kernel Association Test With Multi-Categorical Outcomes](https://doi.org/10.3389/fgene.2022.841764) - [vignette](https://cran.r-project.org/web/packages/MiRKAT/vignettes/MiRKAT_Vignette.html) (Software packages and methods / Linear/Mixed Modeling)
README
# MiRKATMC
The Microbiome Regression-based Kernel Association Test for multi-categorical (nominal or ordinal) data
## Installation
```{r}
# install.packages("devtools") if you have not installed devtools
devtools::install_github("Zhiwen-Owen-Jiang/MiRKATMC")
```
## Usage
We also provided a shiny app which can be accessed at [shiny_MiRKATMC](https://zhiwen-owen-jiang.shinyapps.io/shiny_MiRKATMC/).
```{r}
library(MiRKATMC)
# let's first generate some data
set.seed(123)
test.data <- data.frame(outcome = as.factor(sample(4, 100, replace = TRUE)),
ID = gl(20, 5), time = rep(1:5, 20), age = rnorm(n = 100, mean = 30, sd = 5),
sex = rbinom(100, 1, 1/2))
D1 <- matrix(rbinom(10000, 2, 0.05), 100, 100)
K1 <- crossprod(D1) # kernel matrix
D2 <- matrix(rbinom(10000, 2, 0.1), 100, 100)
K2 <- crossprod(D2) # kernel matrix
K <- list(kernel1 = K1, kernel2 = K2)
K_no_name <- list(K1, K2)
# Then do the analysis
MiRKATMC(formula = outcome ~ age, random = NULL, data.type = 'nominal', Ks = K1, data = test.data)
MiRKATMC(formula = outcome ~ age, random = NULL, data.type = 'ordinal', Ks = K_no_name, data = test.data)
MiRKATMC(formula = outcome ~ age, random = ~ 1 | ID, data.type = 'nominal', Ks = K, data = test.data)
MiRKATMC(formula = outcome ~ age, random = ~ 1 + time | ID, data.type = 'ordinal', Ks = K_no_name, data = test.data)
```
## Getting help
Please email Owen Jiang .
## Citation
Jiang Z, He M, Chen J, Zhao N, Zhan X. MiRKAT-MC: A Distance-Based Microbiome Kernel Association Test With Multi-Categorical Outcomes. Front Genet. 2022 Apr 1;13:841764. doi: 10.3389/fgene.2022.841764.