README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
options(width = 140)
```

# *Mi*xed effects *S*core *T*est <img src="man/figures/mistr.png" align="right" width="120" />

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Test for association between a set of SNPS/genes and continuous or binary outcomes by including variant characteristic information and using (weighted) score statistics.

**Note:**

* From: https://cran.r-project.org/src/contrib/MiST_1.0.tar.gz
* Reference: https://doi.org/10.1002/gepi.21717

## Installation

```{r}
#| eval: false
# Install MiSTr from CRAN:
install.packages("MiSTr")

# Or the the development version from GitHub:
# install.packages("remotes")
remotes::install_github("mcanouil/MiSTr")
```


## MiSTr in Action

```{r}
library(MiSTr)
data(mist_data)
attach(mist_data)
```

### Continuous Outcome

```{r}
res <- mist(
  y = phenotypes[, "y_taupi"],
  X = phenotypes[, paste0("x_cov", 0:2)],
  G = genotypes,
  Z = variants_info[, 1, drop = FALSE]
)
str(res)
print(res)
```

### Binary Outcome

```{r}
res <- mist(
  y = phenotypes[, "y_binary"],
  X = phenotypes[, paste0("x_cov", 0:2)],
  G = genotypes,
  Z = variants_info[, 1, drop = FALSE]
)
str(res)
print(res)
```