Dear @smorabit, thank you for your package, it is very useful to me.
I am writing regarding a simple, but perhaps not so clear, issue. I want to analyze a specific cluster in my dataset. When I run:
seurat_obj <- SetupForWGCNA(
seurat_obj,
gene_select = "fraction", # the gene selection approach
fraction = 0.05, # fraction of cells that a gene needs to be expressed in order to be included
wgcna_name = "tutorial" # the name of the hdWGCNA experiment
)
I am wondering about the gene_select parameter. If I use "fraction", it seems to select genes based on the whole dataset. The same happens with "hvg".
Should I instead use gene_select = "custom" and provide the markers of my cluster of interest (or the HVGs calculated only for that cluster)?
Currently, by selecting "fraction" or "hvg", I get modules that are not specific to my cluster (indeed, I see them everywhere in the UMAP). Could you please guide me in this choice? I would like to discover modules that are specific to my cluster.
Thank you!
Dear @smorabit, thank you for your package, it is very useful to me.
I am writing regarding a simple, but perhaps not so clear, issue. I want to analyze a specific cluster in my dataset. When I run:
I am wondering about the gene_select parameter. If I use "fraction", it seems to select genes based on the whole dataset. The same happens with "hvg".
Should I instead use gene_select = "custom" and provide the markers of my cluster of interest (or the HVGs calculated only for that cluster)?
Currently, by selecting "fraction" or "hvg", I get modules that are not specific to my cluster (indeed, I see them everywhere in the UMAP). Could you please guide me in this choice? I would like to discover modules that are specific to my cluster.
Thank you!