NetRep {NetRep}

Fast permutation procedure for testing network module replication

Description

Functions for assessing the replication/preservation of a network module's topology across datasets through permutation testing. This is suitable for networks that can be meaningfully inferred from multiple datasets. These include gene coexpression networks, protein-protein interaction networks, and microbial interaction networks. Modules within these networks consist of groups of nodes that are particularly interesting: for example a group of tightly connected genes associated with a disease, groups of genes annotated with the same term in the Gene Ontology database, or groups of interacting microbial species, i.e. communities. Application of this method can answer questions such as; (1) do the relationships between genes in a module replicate in an independent cohort? (2) are these gene coexpression modules preserved across tissues or tissue specific? (3) are these modules conserved across species? (4) are microbial communities preserved across multiple spatial locations?

Details

The main function for this package is modulePreservation. Several functions for downstream are also provided: networkProperties for calculating the topological properties of a module, and plotModule for visualising a module.

Author(s)

Maintainer: Scott Ritchie [e-mail] (0000-0002-8454-9548)

See Also

Useful links:

• Report bugs at https://github.com/sritchie73/NetRep/issues