Network creation

Principle

The networkCreation function available in ODAMNet creates two files: a disconnected network (with self loop) and a bipartite network.

Input parameters for network creation

By default, the networkCreation creates a rare disease pathways network (data are retrieved from WikiPathways [1] automatically). The created network is disconnected and contains only self loop (i.e. rare disease pathways linked to themself). The bipartite network connects genes nodes to rare disease pathway nodes.

You can also provided your own pathways/processes of interest using --GMT parameter.

--networksPath PATH

Output folder name where the pathways/processes network is saved [requiered]

--networksName FILENAME

File name to save the pathways/processes network. The created network is in GR format. [default: WP_RareDiseasesNetwork.gr]

--bipartitePath PATH

Output folder name where the bipartite genes-pathways/processes is saved [requiered]

--bipartiteName FILENAME

File name to save the bipartite network. The created network is in GR format. [default: Bipartite_WP_RareDiseases_geneSymbols.gr]

--GMT FILENAME

Tab-delimited file that describes gene sets of pathways/processes of interest. Pathways/processes can come from several sources (e.g. WP and GO:BP). [FORMAT]

-o, --outputPath PATH

Name of the folder to save complementary results (i.e. query results) [default: OutputResults]

Use-case command lines

Data retrieved by queriesData provided by user

odamnet networkCreation --networksPath useCases/InputData/multiplex/2/ \
                        --networksName RareDiseasePathways_network_useCase1.gr \
                        --bipartitePath useCases/InputData/bipartite/ \
                        --bipartiteName Bipartite_RareDiseasePathways_geneSymbols_useCase1.gr \
                        --outputPath useCases/OutputResults_useCase1

References

[1]

Martens M, Ammar A, Riutta A et al.. WikiPathways: connecting communities. Nucleic acids research. 2021.