How to get real cell names from Seurat Object?
1
0
Entering edit mode
7 months ago
leranwangcs ▴ 60

Hi,

I'm trying to extract cell names from my seurat object. I tried

colnames(BAAK_B@assays$RNA@data)  But all I got was: "AATGAAGAGAGCCGTA-1" "ACTATGGGTTGACGGA-1" "ACTGTCCAGGAAGTCC-1" "AGATCGTCACTTGTCC-1" "AGCGTATAGTCTTGGT-1" "AGCGTATCACTCTAGA-1" "AGCTACAGTCCAGCAC-1" "AGCTTCCGTGGCAGAT-1" "AGCTTCCTCAAGTCTG-1" "AGGACTTGTTATTCTC-1"  I wondered if this is what seurat supposed to generate? Or is there any way to get some real cell names? Such as "tuft" cell? Thanks very much! rna-seq • 816 views ADD COMMENT 2 Entering edit mode 7 months ago Do you mean cell type, rather than cell name? Seurat doesn't automatically annotate your cells with the cell type. You can do that through manual intervention with the RenameIdents function, or you can get the SingleR package from bioconductor to "guess" it for you. you can get the current identity with the Idents function. ADD COMMENT 0 Entering edit mode Thanks for the reply! I was confused because in a seurat tutorial, it says there was a column called cellType which looks like this: ## nGene nUMI orig.ident celltypes nCount_RNA nFeature_RNA ## X7873M.1 3563 11796 SeuratProject Macrophage 11796 3563 ## X7873M.104 2670 7570 SeuratProject Macrophage 7570 2670 ## X7873M.105 2241 5510 SeuratProject Macrophage 5510 2241 ## X7873M.106 4705 22636 SeuratProject CAF 22636 4705 ## X7873M.110 3169 11690 SeuratProject Macrophage 11690 3169 ## X7873M.114 4659 20798 SeuratProject Macrophage 20798 4659  and if you run: sort(table(ovarian@meta.data$celltypes))


the output should be something like this:

##  Naive CD4 T Memory CD4 T   CD14+ Mono            B        CD8 T
##          697          483          480          344          271
## FCGR3A+ Mono           NK           DC     Platelet
##          162          155           32           14


However, I don't have the "cellType" column contained in the meta.data slot:

                                               orig.ident.  nCount_RNA nFeature_RNA
AATGAAGAGAGCCGTA-1     BAAK_B       1573          743
ACTATGGGTTGACGGA-1     BAAK_B       5883         2049
ACTGTCCAGGAAGTCC-1     BAAK_B      14083         2945
AGATCGTCACTTGTCC-1     BAAK_B       6661         2211
AGCGTATAGTCTTGGT-1     BAAK_B        520          285


And if I do Idents(BAAK_B) I got something like this:

AATGAAGAGAGCCGTA-1 ACTATGGGTTGACGGA-1 ACTGTCCAGGAAGTCC-1 AGATCGTCACTTGTCC-1
BAAK_B                          BAAK_B                                 BAAK_B                              BAAK_B
AGCTACAGTCCAGCAC-1 AGCTTCCGTGGCAGAT-1 AGCTTCCTCAAGTCTG-1 AGGACTTGTTATTCTC-1
BAAK_B                                   BAAK_B                           BAAK_B                           BAAK_B


And if I use "RenameIdents", I need a list of cell names to assign to the new.ident.name parameter, but could that be done only if I have known which cell type should be assigned to which?

I can try SingleR, but I'm curious if this is a must step to get cell type, why not seen in most of the tutorial? I'm worried if I missed anything so that the cellType column is missing?

Thank you!!

1
Entering edit mode

In the tutorials the cell types were defined previously by a researcher, and are not generated automatically. You need to manually label your clusters/cell types, or use a program like singleR (which was stated above) to infer cell types.

0
Entering edit mode

Thanks very much for your help!!