README.Rmd

# Analysis of coronary artery disease genetic risk and the metabolome in young individuals

## Description
Files for the analysis of the association between coronary artery disease genetic risk and the metabolome in young individuals using data in ALSPAC

Running masterfile.sh (as below) will complete all of the analyses once everything is setup, please note the prerequisites below

masterfile.sh PATH_TO_DIRECTORY METABOLITE_FILE GENOTYPE_FILE COHORT_CHARACTERISTICS_FILE

## Prerequisites
* Access the genotype and metabolomics data from ALSPAC
* The genotype data should be in dosage (bgen) format - if not parts of the R script will have to be altered 
* Within "outputs", directories named "forests", "tables", "heatmaps" and "other" will need to be made if you are to follow the scripts exactly - of course where the results are outputted and the names of the outputs can be easily changed within the scripts

## Main outputs

* qqplot showing the association between the metabolites and the CAD-GRS
* violin plot showing how the association between the GRS and lipoproteins differs between lipoprotein subgroups 
* heatmaps showing 1. association between all SNPs and all metabolites and 2. association between SNPs in _HMGCR_ locus + all SNPs associated with 1 or more metabolites (FDR < 0.05) 
* age sensitivity analyses plots
* tables of association