Analysis scripts and full summary statics data of the manuscript "Whole-exome rare variant analysis of Alzheimer’s disease and related biomarker traits" by Küçükali et al., Alzheimer's and Dementia (2022), https://doi.org/10.1002/alz.12842 .
This repository contains the full association results of our study, together with the gene-based rare variant association analysis scripts used to generate (PLINKSKAT.R & PLINKMetaSKAT.R) and annotate & visualize (Annotate_PLINKSKAT_Results.R & Annotate_PLINKMetaSKAT_Results.R) these results.
More details and descriptions of these are available in respective subdirectories association_results and analysis_scripts.
You can use the provided conda
environment file environment_plinkskat.yml to create an environment and load these packages in this environment. You can also clone the repository and add the R scripts into this environment:
git clone https://github.com/SleegersLab-VIBCMN/AD_Biomarkers_RareVariantAnalyses.git
conda env create -f analysis_scripts/environment_plinkskat.yml
conda activate plinkskat
ln -s analysis_scripts/*.R ~/miniconda3/envs/plinkskat/bin/.
Or alternatively, using mamba
:
git clone https://github.com/SleegersLab-VIBCMN/AD_Biomarkers_RareVariantAnalyses.git
mamba env create -f environment_plinkskat.yml
mamba activate plinkskat
ln -s analysis_scripts/*.R ~/miniconda3/envs/plinkskat/bin/.
After this, you can execute the R scripts (PLINKSKAT.R, PLINKMetaSKAT.R, Annotate_PLINKSKAT_Results.R, and Annotate_PLINKMetaSKAT_Results.R) directly from the command line. For more information, see analysis_scripts subdirectory.