This is a wrapper for MAGMA, to easily analyze pathways from MSigDB and selected "psychiatric pathways" (link to pathway source is provided in the programme), Open Targets, gene families and drug gene-sets (reference soon to be available; if you want to use the drug results/data, please contact us).
1- Clone repository.
2- Download ancestry reference directory (g1000_ref.tar.gz). Decompress it inside main directory.
3- Inside main directory, install packages by running "./InstallPackages.sh"
4- Simple command to run all pathways: ./runPath.sh nameofgwas nameofoutput samplesize
Example: ./runPath.sh example_GWAS/Alzheimer ./example 10000
If you want to use the drug data in your paper, please contact us (helena.gaspar@kcl.ac.uk). If you use our scripts for your paper, please remember to cite us (https://github.com/hagax8/PathAnalyzor, by Héléna A. Gaspar, Social, Genetic & Developmental Psychiatry Centre, King's College London)
Main output files:
1- HTML files: result tables and bubble plots
2- xls file: gathering all gene-wise and pathway results
3- pdf files: gene pathway qq plots, top genes and pathways, gene manhattan plot