HOGImine (Higher-Order Genetic Interaction miner), is a pattern-mining-based algorithm for finding genetic meta-markers, i.e. combinations of genetic markers, that show a statistical association with a phenotype. Compared to the state-of-the-art miners, it expands the class of discoverable genetic meta-markers by considering higher-order interactions of genes and by allowing multiple encodings for the genetic variants. Moreover, our method can exploit prior biological knowledge on gene interactions, such as protein-protein interaction networks, genetic pathways and protein complexes, to restrict its search space.
We provide two versions, HOGImine-binary, that accepts binary encodings for the markers, and HOGImine-additive, that accepts additive encodings.
Compilation uses make. Currently the code is compiled with gcc-12, but other compilers might work as well.
cd HOGImine-binary
make
The options for HOGImine-binary are:
-
-i file: marker file -
-l file: labels file -
-s file: snp names file -
-c file: covariate file -
-m file: snp map file -
-e file: edge file -
-f level: target fwer -
-o file: output file name -
-p p: number$p$ of permutations (default$0$ ), if$p > 0$ it runs a permutation testing procedure -
-d d: maximum interval length -
-v: outputs all the testable patterns
The options for HOGImine-additive are the same, with the following changes:
-i file: marker (with dominant encoding) file-h file: marker (with recessive encoding) file
./HOGImine-binary/hogimine_binary -i data/athaliana/interactome_0kb/avrRpm1/avrRpm1_X.txt -l data/athaliana/interactome_0kb/avrRpm1/avrRpm1_Y.txt -c data/athaliana/covar_snps/avrRpm1/avrRpm1_covar_n2.txt -s data/athaliana/interactome_0kb/avrRpm1/avrRpm1_snpID.txt -m data/athaliana/interactome_0kb/avrRpm1/avrRpm1_snp_map.txt -e data/athaliana/athal_ppi/interactome/AI_interactions_genes.txt -f 0.05 -o out_athaliana