README.md

In belleau/subnetsim: Validating that a specific subnetwork has significantly more interactions than expected by randomness

subnetsim : Validating that a specific subnetwork has significantly more interactions than expected by randomness

The R subnetsim package implements a simulation analysis, based on bootstrapping, for testing the hypothesis that a selected subnetwork, which is part of a larger network, has more interactions than expected by randomness. To do so, subnetworks with the same number of nodes than the tested subnetwork are randomly generated by bootstrapping. Three measures of connectivity used to validate the hypothesis are:

• the number of nodes in the subnetwork including all the first-degree neighbor nodes
• the number of links in the subnetwork including all the links of the first-degree neighbor nodes
• the number of links in the subnetwork

The R subnetsim package also offers the possibility to easily graph the results of the simulations.

Citing

If you use this package for a publication, we would ask you to cite the following:

Belleau P, Deschênes A, Boutchueng-Djidjou M et Faure R L. Validating that a specific subnetwork has significantly more interactions than expected by randomness. protocols.io. DOI: 10.17504/protocols.io.sdqea5w, https://dx.doi.org/10.17504/protocols.io.sdqea5w

Boutchueng-Djidjou M, Belleau P, Bilodeau N, Fortier S, Bourassa S, Droit A, Elowe S, et Faure R L. (2018) A type 2 diabetes disease module with a high collective influence for Cdk2 and PTPLAD1 is localized in endosomes. PLoS ONE 13(10): e0205180. DOI: 10.1371/journal.pone.0205180, https://doi.org/10.1371/journal.pone.0205180

Authors

Pascal Belleau, Astrid Deschênes, Martial Boutchueng-Djidjou and Robert L. Faure

License

This package and the underlying subnetsim code are distributed under the Artistic license 2.0. You are free to use and redistribute this software.

For more information on Artistic 2.0 License see http://opensource.org/licenses/Artistic-2.0

Bugs/Feature requests

If you have any bugs or feature requests, let us know.

Thanks!

belleau/subnetsim documentation built on May 27, 2019, 2:08 p.m.