Co-Receptor Expression #454
Description
I know I am listing a lot issues lol. So I just figured this out. So for a lot of the pathways the database has multiple genes listed for the receptors, i.e one receptor and a couple co-receptor. I noticed that when I ran identifyOverexpressionGenes the genes of interest that I wanted was in the cellchat, however the coreceptor expression was nonexistent, which lead to the pathway interaction that I am interested in not being present in the cellchat. I dont think that if the coreceptor expression is 0 that the pathway should just be thrown out in computeCommunProb as some genes could just be lowly expressed or randomly drop out in rnaseq. Is there away around this aside from just updating the database to include the pathways that only have the ligand and receptor with no other subunits or coreceptors? Could there be a Cellchatdatabase v3 that addresses this? I think this is especially pertinent for Xenium and Visium as they only include a panel of genes.