mass-a
commented
5 months ago Hello! I think it's not feasible to use signatures that span multiple assays. This is because UCell scores are based on ranks, and RNA and ADT readouts are not directly comparable (both in scale and number of features).
My suggestion would be to evaluate RNA and ADT signatures separately, and then combine the resulting UCell scores. For instance, using your example:
markers_RNA <- list()
markers_RNA$Tcell_Tcm_RNA <- c("CD3D+","CD69-","CCR7+","SELL+","KLF2+","IL7R+")
markers_ADT <- list()
markers$Tcell_Tcm_ADT <- c("CD3+","CD69-","CD197+","CD194+")
obj <- AddModuleScore_UCell(obj, features=markers_RNA, assay="RNA")
obj <- AddModuleScore_UCell(obj, features=markers_ADT, assay="ADT", maxRank=50)(note that you probably need to lower the default maxRank e.g. to 50, to account for the fact that the protein panel is smaller than the space of all genes). You will obtain separate UCell scores based on the RNA and ADT, which you could then combine e.g. by averaging.
Hello!
I am trying to learn this tool and apply it to my seeurat object, it has problems with the gene names i give for the gene sets. the code: `markers <- list() markers$Tcell_Tcm <- c("ADT_CD3+","rna_CD3D+","ADT_CD69-","rna_CD69-","ADT_CD197+","rna_CCR7+","rna_SELL+","rna_KLF2+","ADT_CD194+","rna_CCR4+","rna_IL7R+")
markers$Tcell_CD4_Tem <- c("ADT_CD3+","rna_CD3D+","ADT_CD4+","rna_CD4+","ADT_CD8-","rna_CD8A-","ADT_CD69-","rna_CD69-","ADT_CD45RO+","ADT_CD197-","rna_CCR7-","rna_SELL-","rna_SELPLG+","ADT_CD194+","rna_CCR4+","rna_F13A1+","rna_MRC1+","rna_LYVE1+") #,"rna_F13A1+","rna_MRC1+","rna_LYVE1+" markers$Tcell_CD8_Tem <- c("ADT_CD3+","rna_CD3D+","ADT_CD4-","rna_CD4-","ADT_CD8+","rna_CD8A+","ADT_CD69-","rna_CD69-","ADT_CD45RO+","ADT_CD197-","rna_CCR7-","rna_SELL-","rna_SELPLG+","ADT_CD194+","rna_CCR4+","rna_F13A1+","rna_MRC1+","rna_LYVE1+") #,"rna_F13A1+","rna_MRC1+","rna_LYVE1+"
markers$Tcell_CD4_Trm_ITGA1pos_ITGAEpos <- c("ADT_CD3+","rna_CD3D+","ADT_CD4+","rna_CD4+","ADT_CD8-","rna_CD8A-","ADT_CD69+","rna_CD69+","rna_ITGAE+","ADT_CD45RO+","rna_ITGA1+","rna_SELPLG+","ADT_CD197-","rna_CCR7-","rna_SELL-","ADT_CD194+","rna_CCR4+","rna_EOMES+","rna_RUNX3+","rna_ZNF683+","rna_PRDM1+","rna_AHR+") markers$Tcell_CD4_Trm_ITGA1neg_ITGAEpos <- c("ADT_CD3+","rna_CD3D+","ADT_CD4+","rna_CD4+","ADT_CD8-","rna_CD8A-","ADT_CD69+","rna_CD69+","rna_ITGAE+","ADT_CD45RO+","rna_ITGA1-","rna_SELPLG+","ADT_CD197-","rna_CCR7-","rna_SELL-","ADT_CD194+","rna_CCR4+","rna_EOMES+","rna_RUNX3+","rna_ZNF683+","rna_PRDM1+","rna_AHR+") markers$Tcell_CD8_Trm_ITGA1pos_ITGAEpos <- c("ADT_CD3+","rna_CD3D+","ADT_CD8+","rna_CD8A+","ADT_CD4-","rna_CD4-","ADT_CD69+","rna_CD69+","rna_ITGAE+","ADT_CD45RO+","rna_ITGA1+","rna_SELPLG+","ADT_CD197-","rna_CCR7-","rna_SELL-","ADT_CD194+","rna_CCR4+","rna_EOMES+","rna_RUNX3+","rna_ZNF683+","rna_PRDM1+","rna_AHR+") markers$Tcell_CD8_Trm_ITGA1neg_ITGAEpos <- c("ADT_CD3+","rna_CD3D+","ADT_CD8+","rna_CD8A+","ADT_CD4-","rna_CD4-","ADT_CD69+","rna_CD69+","rna_ITGAE+","ADT_CD45RO+","rna_ITGA1-","rna_SELPLG+","ADT_CD197-","rna_CCR7-","rna_SELL-","ADT_CD194+","rna_CCR4+","rna_EOMES+","rna_RUNX3+","rna_ZNF683+","rna_PRDM1+","rna_AHR+")
markers$Tcell_CD4_Trm_ITGA1pos_ITGAEneg <- c("ADT_CD3+","rna_CD3D+","ADT_CD4+","rna_CD4+","ADT_CD8-","rna_CD8A-","ADT_CD69+","rna_CD69+","rna_ITGAE-","ADT_CD45RO+","rna_ITGA1+","rna_SELPLG+","ADT_CD197-","rna_CCR7-","rna_SELL-","ADT_CD194+","rna_CCR4+","rna_EOMES+","rna_RUNX3+","rna_ZNF683+","rna_PRDM1+","rna_AHR+") markers$Tcell_CD4_Trm_ITGA1neg_ITGAEneg <- c("ADT_CD3+","rna_CD3D+","ADT_CD4+","rna_CD4+","ADT_CD8-","rna_CD8A-","ADT_CD69+","rna_CD69+","rna_ITGAE-","ADT_CD45RO+","rna_ITGA1-","rna_SELPLG+","ADT_CD197-","rna_CCR7-","rna_SELL-","ADT_CD194+","rna_CCR4+","rna_EOMES+","rna_RUNX3+","rna_ZNF683+","rna_PRDM1+","rna_AHR+") markers$Tcell_CD8_Trm_ITGA1pos_ITGAEneg <- c("ADT_CD3+","rna_CD3D+","ADT_CD8+","rna_CD8A+","ADT_CD4-","rna_CD4-","ADT_CD69+","rna_CD69+","rna_ITGAE-","ADT_CD45RO+","rna_ITGA1+","rna_SELPLG+","ADT_CD197-","rna_CCR7-","rna_SELL-","ADT_CD194+","rna_CCR4+","rna_EOMES+","rna_RUNX3+","rna_ZNF683+","rna_PRDM1+","rna_AHR+") markers$Tcell_CD8_Trm_ITGA1neg_ITGAEneg <- c("ADT_CD3+","rna_CD3D+","ADT_CD8+","rna_CD8A+","ADT_CD4-","rna_CD4-","ADT_CD69+","rna_CD69+","rna_ITGAE-","ADT_CD45RO+","rna_ITGA1-","rna_SELPLG+","ADT_CD197-","rna_CCR7-","rna_SELL-","ADT_CD194+","rna_CCR4+","rna_EOMES+","rna_RUNX3+","rna_ZNF683+","rna_PRDM1+","rna_AHR+") `
The seurat object is for a CITE-seq dataset, the gene names work in other functions (also tried without the assay keys), most likely i am doing something wrong but did not figure out what.
Thanks for any help