How to refine signaling input into a handful of clusters out of many.

[kasumaz]

Dear Developers,

I could have CellCall up and running on a seurat object. Within this object, I have about 25 different clusters. This is a bit of a limited dataset where i have another dataset that is even larger with more clusters. The main cell clusters I am interesting in, there are about 8 clusters which I aim to focus onto. Within these 8 clusters i would want to try to figure out how they receive input and the downstream TFs-TGs, pathways and anything else. Is there a way to refine the script so that the analysis only looks at what these 8 clusters receive as signals, TFs, pathways, etc?

At the stage of running "TransCommuProfile" its taken 2 hours but i see combinations of senders and receivers that are not interesting or biologically relevant.

Many thanks. K

[ShellyCoder]

Hi there, I hope this would not be late for this reply.

Accutally, we recommend the embedding method subset in package Seurat to abstract interested sub_object. A demo command follows:

subset(x = pbmc, idents = c('CD4 T cells', 'CD8 T cells'), invert = TRUE)

reference to https://github.com/satijalab/seurat/issues/3108

Thanks for your contributions!

Yours sincerely.