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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 best pipeline of hdWGCNA for single-cell data analysis #196

Closed yizhang-zoey closed 3 months ago

yizhang-zoey commented 4 months ago

I have a single cell data containing 10 cell types. All 10 cell types share the same per-processing (wgcna genes selection and define metacells on each cell type): SetupForWGCNA, MetacellsByGroups. But the following step about co-expression analysis (SetDatExpr, ConstructNetwork) only for on cell type such as "INH":

seurat_obj <- ConstructNetwork(
    seurat_obj, 
    tom_name = 'INH',  # name of the topoligical overlap matrix written to disk
   ...
)

I want to save the co-expression result of 10 cell types respectively in seurat_obj@misc with the respective cell type name. What is the best work pipeline?

smorabit commented 4 months ago

Hi,

I will link you to a previous issue asking a similar question. You are either going to want to write a loop or run a separate script for each cell type.

Previous issue: #82