https://github.com/kenhanscombe/associatr

Genetic Association Plots
https://github.com/kenhanscombe/associatr

genetic-association-plots kcl-sgu manhattan-plot region-plot

Last synced: 18 days ago
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Genetic Association Plots

• Host: GitHub
• URL: https://github.com/kenhanscombe/associatr
• Owner: kenhanscombe
• License: other
• Created: 2020-03-31T15:47:15.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2020-11-01T11:52:59.000Z (about 4 years ago)
• Last Synced: 2024-11-09T23:32:00.394Z (3 months ago)
• Topics: genetic-association-plots, kcl-sgu, manhattan-plot, region-plot
• Language: R
• Homepage:
• Size: 657 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        

# associatr: Genetic Association Plots

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

[![Travis build status](https://travis-ci.com/kenhanscombe/associatr.svg?branch=master)](https://travis-ci.com/kenhanscombe/associatr)

[![Codecov test coverage](https://codecov.io/gh/kenhanscombe/associatr/branch/master/graph/badge.svg)](https://codecov.io/gh/kenhanscombe/associatr?branch=master)

## Overview

associatr is an R package for manhattan and regional plots. By default

only variants with p < 0.001 are plotted in the manhattan plot. Region

plots use LDlinkR to retrieve LD and SQL queries to UCSC genome browser

to get biological context.

## Installation

```{R}

devtools::install_github("kenhanscombe/associatr", dependencies = TRUE, force = TRUE)

```

**Note**. `region` requires an

[LDlinkR personal access token](https://cran.r-project.org/web/packages/LDlinkR/vignettes/LDlinkR_vignette_v8-2_TM.html).

[Request token](https://ldlink.nci.nih.gov/?tab=apiaccess.).