Find Markers of Disease

[cmarsac]

Dear Satija Lab,

I am currently trying to use the FindMarkers() function to find the markers of a given disease state. I was able to add the disease states to the Seurat object metadata and have tried coding it as a factor and a numeric but when I set the ident.1 argument equal to the disease state it returns "Cannot find the following identities in the object:" Please advise.

[timoast]

Can you include the full code you're running?

[cmarsac]

Thank you for your reply. The code is as follows:

1 library(Seurat)
2 data<-readRDS("/counts.RDS") #sc-rnaseq counts
3 annotation<-readRDS("/annotation.RDS") #corresponding patient info, disease state, etc. for each cell
4 all.genes<-rownames(data)
5
6 seurat<-CreateSeuratObject(data)
7 [email protected][["status"]]<-annotation$status #status is a factor where status1, status2, status3, etc. represent various disease states
8
9 seurat<-NormalizeData(seurat)
10 seurat<-FindVariableFeatures(seurat)
11
12 seurat<-ScaleData(seurat, features=all.genes)
13 seurat<-RunPCA(seurat, features=all.genes, npcs=50)
14
15 seurat<-FindNeighbors(seurat)
16 seurat<-FindClusters(seurat)
17
18 seurat<-RunTSNE(seurat, reduction="pca", set.seed(1234), check_duplicates=FALSE)
19
20 markers<-FindAllMarkers(seurat, only.pos=FALSE, min.pct=0, logfc.threshold=0, ident.1="status1")

This is the error that I have been getting:
Error in WhichCells.Seurat(object = object, idents = ident.1) :
Cannot find the following identities in the object: 1

I have also tried coding status as a numeric and a character variable, as well as running [email protected]<[email protected][["status"]] before running FindAllMarkers().

[timoast]

ident.1 is not a parameter in the FindAllMarkers() function, since the function will evaluate each set of cell identities present. The issue here is that you haven't set the active cell identities to the "status" variable that you want to group cells by. You can change the active identities using the Idents<- function. Alternatively, if you want to find markers for one group of cells only, you can use the FindMarkers() function which will let you set the ident.1 and group.by parameters.

[cmarsac]

Thank you for your help. Using the Idents() function seems to have solved my problem.