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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/plinkQC)](https://cran.r-project.org/package=plinkQC)
[![Build Status](https://travis-ci.org/meyer-lab-cshl/plinkQC.svg?branch=master)](https://travis-ci.org/meyer-lab-cshl/plinkQC)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
[![Downloads](http://cranlogs.r-pkg.org/badges/grand-total/plinkQC?color=blue)](https://cran.r-project.org/package=plinkQC)
## <i class="fa fa-map" aria-hidden="true"></i> plinkQC
**plinkQC** is a R/CRAN package for **genotype quality control** in genetic
association studies. It makes PLINK basic statistics (e.g.missing genotyping
rates per individual, allele frequencies per genetic marker) and relationship
functions easily accessible from within R and allows for automatic evaluation
of the results.
Full documentation is available at http://meyer-lab-cshl.github.io/plinkQC/.
**plinkQC** generates a per-individual and per-marker quality control report.
A step-by-step guide on how to run these analyses can be found
[here](https://meyer-lab-cshl.github.io/plinkQC/articles/plinkQC.html).
Individuals and markers that fail the quality control can subsequently be
removed with **plinkQC** to generate a new, clean dataset.
**plinkQC** facilitates an ancestry check for study individuals based on
comparison to reference datasets. The processing of the reference datasets is
documented in detail
[here](https://meyer-lab-cshl.github.io/plinkQC/articles/AncestryCheck.html).
Removal of individuals based on relationship status via **plinkQC** is optimised
to retain as many individuals as possible in the study.
## <i class="fa fa-rocket" aria-hidden="true"></i> Installation
The current github version of **plinkQC** is: 0.3.3 and can be
installed via
```{r github install, eval=FALSE}
library(devtools)
install_github("meyer-lab-cshl/plinkQC")
```
The current CRAN version of **plinkQC** is: 0.3.2 and can be
installed via
```{r install, eval=FALSE}
install.packages("plinkQC")
```
A log of version changes can be found [here](news/index.html).
## <i class="fa fa-pencil" aria-hidden="true"></i> Citation
Meyer HV (2018) plinkQC: Genotype quality control in genetic association
studies. doi:10.5281/zenodo.3373798