Question about the possibility of using external metacell asssignment

[pmandros]

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]

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]

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!