Recommendations for Protein Network Data Structure
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Dario Strbenac ★ 1.5k
@dario-strbenac-5916
Last seen 7 days ago
Australia

If I would like to represent a protein sub-network, what is the best data structure for it? It has the flat file format:

 

Hub Interactor
ABC XYZ
ABC WNT
BCL1 RST
BCL1 DEF
BCL1 ZZY
BCL1 CDF


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.

AnnotationDbi Bimap Interactome • 456 views
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is the infrastructure in ppiStats package relevant?  graph package seems pretty relevant, you can annotate nodes and edges very generally.

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