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