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smorabit / hdWGCNA

High dimensional weighted gene co-expression network analysis
https://smorabit.github.io/hdWGCNA/
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Question about the possibility of using external metacell asssignment #310

Open pmandros opened 2 months ago

pmandros commented 2 months ago

Let's assume that we already have a metacell assignment for the cells, e.g., in the form of a vector. Is it possible to use this assignment such that hdWGCNA creates the metacells and aggregates the expression? Such a feature would be useful if we apriori know a metacell assignment and we want to use hdWGCNA for network analysis.

smorabit commented 2 months ago

Hi, thanks for your question. Please see this vignette regarding the use of alternative metacell approaches.

Note that we did not benchmark which metacell approach is "best" for hdWGCNA, so I believe it is fair to use alternative approaches as you see fit. In our paper we did see "similar" modules for 3 different metacell approaches, (hdWGCNA, SEAcells, and Metacell2).

pmandros commented 2 months ago

Hey, thank you for your fast reply, I really appreciate it. I did stumble upon this informative and useful vignette. What I had in mind was more of using just an assignment of metacells and nothing else. My concrete use case is that I have a single-cell dataset that is already processed with metacell assignment, i.e., I know for each single cell in which metacell they belong. I would like to use this metacell assignment with hdWGCNA, and let hdWGCNA do the aggregation using the assignment. Thank you!