This repository contains scripts used to perform a colocalisation analysis using the REM sleep behavior disorder (RBD) GWAS and two eQTL datasets:
If you use any of the code or data from this repository, please cite our paper. Further, if you use any of the software used within this repository (e.g. coloc, colochelpR, etc.) please make sure to cite the software appropriately.
The code in this repository is released under an MIT license. This repository is distributed in the hope that it will be useful to the wider community, but without any warranty of any kind. Please see the LICENSE file for more details.
Scripts and results of analyses have been described in the following workflows:
- RBD_coloc.Rmd:
Rmddetailing coloc set up and analysis of results. - RBD_coloc_tissue_cell_specificity.Rmd:
Rmddetailing tissue- and cell-type-specificity of genes identified by coloc. - RBD_manuscript_figures:
Rmddetailing code used to produce manuscript figures pertaining to coloc analyses.
All can be view interactively at: https://rhreynolds.github.io/RBD-GWAS-analysis/
Within this repository you will otherwise find:
| Directory | Description |
|---|---|
| docs | Contains all .Rmds and their corresponding .htmls describing analyses performed for this project. These can be view interactively at: https://rhreynolds.github.io/RBD-GWAS-analysis/ |
| logs | For any scripts that were run outside of an .Rmd (e.g. scripts from the scripts directory), a log file was recorded and can be accessed here. |
| manuscript | Figures and tables produced for the manuscript. |
| results | Results from all analyses. |
| scripts | Contains analysis scripts. Each script contains a one-line description and is also referenced in its corresponding .Rmd. |
| R | Various functions called in docs and scripts. |