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Building genesets

Supported databases: OMIM, HGMD, GWASCAT, GO

Disease genes from OMIM, propagated with Disease Ontology

python flib/utils/build_genesets.py -o disease.gmt -d OMIM -p

Human gene ontology, biological process genes, filtered by experimental evidence

python flib/utils/build_genesets.py -o gene-ontology.gmt -d GO -n biological_process -e EXP IDA IPI IMP IGI IEP -p

Run linear SVM prediction with a functional network

Disease gene prediction:

python flib/utils/svm.py -i [global_average.dab] -o [out dir] -g disease.gmt -s files/do_slim.txt -y DO -a

Biological process prediction:

python flib/utils/svm.py -i [global_average.dab] -o [out dir] -g go.gmt -s files/go_neg_slim.txt -y GO -a

Evaluating SVM performance

python flib/utils/evaluate.py -d [svm output dir]