https://github.com/mcanouil/mistr

Mixed effects Score Test
https://github.com/mcanouil/mistr

r r-package r-stats rare-variant-analysis statistics

Last synced: 6 months ago
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Mixed effects Score Test

• Host: GitHub
• URL: https://github.com/mcanouil/mistr
• Owner: mcanouil
• License: lgpl-2.1
• Created: 2019-11-29T16:57:59.000Z (over 5 years ago)
• Default Branch: main
• Last Pushed: 2022-12-05T20:24:29.000Z (over 2 years ago)
• Last Synced: 2023-02-26T05:56:14.433Z (over 2 years ago)
• Topics: r, r-package, r-stats, rare-variant-analysis, statistics
• Language: R
• Homepage: https://m.canouil.fr/MiSTr/
• Size: 20 MB
• Stars: 0
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.Rmd
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE.md
  • Code of conduct: .github/CODE_OF_CONDUCT.md

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README

        
---

output: github_document

---

```{r, echo = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>"

)

options(width = 140)

```

# *Mi*xed effects *S*core *T*est 

[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)

[![GitHub tag](https://img.shields.io/github/tag/mcanouil/MiSTr.svg?label=latest tag)](https://github.com/mcanouil/MiSTr)

[![Codecov test

coverage](https://codecov.io/gh/mcanouil/MiSTr/branch/main/graph/badge.svg)](https://codecov.io/gh/mcanouil/MiSTr?branch=main)

[![R-CMD-check](https://github.com/mcanouil/MiSTr/workflows/R-CMD-check/badge.svg)](https://github.com/mcanouil/MiSTr/actions)

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)

```