If I would like to represent a protein sub-network, what is the best data structure for it? It has the flat file format:
I have considered
Bimap but its vignette is marked as Deprecated so it doesn't seem suitable for the future.
GeneSetCollection seems appealing for this use case. I am developing an analysis framework rather than a specific analysis, so I'd prefer to be using something named more generically, such as
FeatureSetCollection. The features comprising the network are not required to be genes so I don't want to give users the impression that they must be.