This is the github repository for the Python version of BridGE

To run: python3 bridge.py --job=DataProcess --options

Options: --plinkFile = path to plink input file without extention. --geneAnnotation = path to gene annotation file --genesets = path to geneset reference --mappingDistance = SNP to Gene mapping distance(in bp) --maxPath = maximum number of SNPs in a pathway --minPath = Minimum number of SNPs in a pathway Example: python3 bridge.py --job=DataProcess --plinkFile=data/gwas_data_final

To run: python3 bridge.py --job=ComputeInteraction --options

Options: --model = model, RR - RD - DD - combined --nWorker = number of parallel workers --samplePerms = number of sample permuations Example: python3 bridge.py --job=ComputeInteraction --model=RR --nWorker=6 --samplePerms=10

To run: python3 bridge.py --job=ComputeInteraction --options

Options: --model = model, RR - RD - DD - combined --nWorker = number of parallel workers --samplePerms = number of sample permuations --snpPerms = number of snp permutations used in generatin pathway stats --binaryNetwork = Binary flag to use binarized interactions