search

sqjin / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
GNU General Public License v3.0
642 stars 145 forks source link

CellChat LR database questions #297

Open smk5g5 opened 3 years ago

smk5g5 commented 3 years ago

Hi,

I was looking at the contents of cellchat ligand receptor data rds. It was my understanding is that ligand name and gene symbol info should be the same in cellchat_data$interaction$ligand and cellchat_data$geneInfo$Symbol what to do when it is not?

e.g : 

>setdiff(unique(cellchat_data$interaction$ligand),cellchat_data$geneInfo$Symbol)
 [1] "Activin AB"     "Inhibin A"      "Inhibin B"      "IL12AB"
 [5] "IL23 complex"   "IL27 complex"   "IL17AF"         "LTa1b2"
 [9] "Npnt complex 1" "Npnt complex 2" "ITGA4_ITGB1"    "ITGA9_ITGB1"
[13] "ITGA4_ITGB7"

I was trying to look at the expression of ligands in my bulk RNAseq datasets thus I pulled the ligand receptor rds object in cellchat and noticed that discrepancy and I was wondering how cellchat handles it?

Thanks!

sqjin commented 3 years ago

@smk5g5 These are complex and thus contain multiple genes. You can find the associated genes for one complex in cellchat_data$complex. You can also access it via 

complex <- object@DB$complex
geneInfo <- object@DB$geneInfo

geneL <- unique(pairLR$ligand) geneL <- extractGeneSubset(geneL, complex, geneInfo)