https://github.com/umr1283/rain

Reference-based Ancestry INference
https://github.com/umr1283/rain

ancestry-inference ethnicity-analysis genomics r r-package r-stats

Last synced: 3 months ago
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Reference-based Ancestry INference

• Host: GitHub
• URL: https://github.com/umr1283/rain
• Owner: umr1283
• License: other
• Created: 2020-01-16T12:53:58.000Z (about 5 years ago)
• Default Branch: main
• Last Pushed: 2022-12-01T15:25:35.000Z (about 2 years ago)
• Last Synced: 2024-08-13T07:14:08.231Z (6 months ago)
• Topics: ancestry-inference, ethnicity-analysis, genomics, r, r-package, r-stats
• Language: R
• Homepage:
• Size: 1.83 MB
• Stars: 3
• Watchers: 1
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.Rmd
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: .github/CODE_OF_CONDUCT.md
  • Codeowners: .github/CODEOWNERS

Awesome Lists containing this project

• jimsghstars - umr1283/rain - Reference-based Ancestry INference (R)

README

        
---

output: github_document

---

```{r, echo = FALSE}

knitr::opts_chunk$set(

  eval = FALSE,

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```

# Reference-based Ancestry INference 

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

[![GitHub tag](https://img.shields.io/github/tag/umr1283/rain.svg?label=latest tag&include_prereleases)](https://github.com/umr1283/rain)

[![R build status](https://github.com/umr1283/rain/workflows/R-CMD-check/badge.svg)](https://github.com/umr1283/rain/actions)

## Installation

```{r, eval = FALSE}

# Install rain from CRAN:

install.packages("rain")

# Or the the development version from GitHub:

# install.packages("remotes")

remotes::install_github("umr1283/rain")

```

## Overview 

* `estimate_ethnicity()` allows to format VCF files and compute the genomic components (and some figures) for ethnicity using [flashpca](https://github.com/gabraham/flashpca) software

* `pca_report()` allows to compute an analysis report using principal component analysis from [flashpca](https://github.com/gabraham/flashpca) software. 

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## Getting help

If you encounter a clear bug, please file a minimal reproducible example on [github](https://github.com/umr1283/rain/issues).  

For questions and other discussion, please contact the package maintainer.

## Code of Conduct

Please note that the `rain` project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.