Here I show how to make a regional association plot of some data. We will also create a MIAMI style plot. And lastly we will check out the co-localization of the genetic signal to answer the question whether the signals in two different GWAS overlap.
You can load this project in RStudio by opening the file called 'racer_coloc_tutorial.Rproj'.
| File | Description | Usage |
|---|---|---|
| README.md | Description of project | Human editable |
| LICENSE | User permissions | Read only |
| racer_coloc_tutorial.Rproj | Project file | Loads project |
| .worcs | WORCS metadata YAML | Read only |
| renv.lock | Reproducible R environment | Read only |
| report/report.rmd | Source code for paper | Human editable |
| report/references.bib | BibTex references for manuscript | Human editable |
| images | Generic images directory | Human editable |
| scripts | Generic scripts directory | Human editable |
| scripts/run_me.R | Script to run analyses | Human editable |
| scripts/prepare_data.R | Script to process raw data | Human editable |
| scripts/functions.R | Some generic functions | Human editable |
| scripts/create_worcs.R | To create WORCS project | Human editable |
This project uses the Workflow for Open Reproducible Code in Science (WORCS) to ensure transparency and reproducibility. The workflow is designed to meet the principles of Open Science throughout a research project.
To learn how WORCS helps researchers meet the TOP-guidelines and FAIR principles, read the preprint at https://osf.io/zcvbs/
- To get started with
worcs, see the setup vignette - For detailed information about the steps of the WORCS workflow, see the workflow vignette
Please refer to the vignette on reproducing a WORCS project for step by step advice.
Dr. Sander W. van der Laan is funded through grants from the Netherlands CardioVascular Research Initiative of the Netherlands Heart Foundation (CVON 2011/B019 and CVON 2017-20: Generating the best evidence-based pharmaceutical targets for atherosclerosis [GENIUS I&II]). We are thankful for the support of the ERA-CVD program ‘druggable-MI-targets’ (grant number: 01KL1802), the EU H2020 TO_AITION (grant number: 848146), and the Leducq Fondation ‘PlaqOmics’.
The framework was based on the WORCS package.
_Version:_ v1.0.0</br>
_Last update:_ 2022-03-08</br>
_Written by:_ Sander W. van der Laan (s.w.vanderlaan-2[at]umcutrecht.nl).
* v1.0.0 Initial version.
Copyright (c) 1979-2022 Sander W. van der Laan | s.w.vanderlaan [at] gmail [dot] com.
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