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I am aware of this question Manually define clusters in Seurat and determine marker genes that is similar but I couldn't make tit work for my use case.

So I have a single cell experiments and the clustering id not great I have a small groups of 6 cells (I know it is extremely small, but nonetheless I would like to make the most of it) that are clearly isolate in UMAP and display marker that I am interresting in.

I managed to get those cells names in barcode (e.g.: AGCCAGCTCGCTTTAT).

I would like to compute differential expression of those cells against all others groups (using FindMarkers or FindAllMarkers).

I tried to manually define the cluster in: Seurat_obj@meta.data$seurat_clusters But using FindMarkers (it says this groups don't exist)

then I try to modify s_19270BC@active.ident

but then it could not found metadata attached to my newly define group.

I am kind of stuck and any help is warmly welcome

Code

My R is quite rusty...

names_ # a vector with the names of the cell I want as a cluster

my seurat object have 5 cluster 0..4. So I want to add a 6th clusters with id 5


#First attempt manually modify the vector active.ident and cluster


they are both factor so we need to add a factor level


levels(seurat_obj@active.ident) = c(levels(seurat_obj@active.ident), 5)
levels(seurat_obj@meta.data$seurat_clusters) = c(levels(seurat_obj@meta.data$seurat_clusters), 5)


then modify them :


seurat_obj@active.ident[which(row.names(seurat_obj@meta.data) %in%  names_)] = 5
seurat_obj@meta.data$seurat_clusters[which(row.names(seurat_obj@meta.data) %in%  names_)] = 5


FindMarkers(s_19270BC, ident.1 = 5)

So This morning it works... I don't know what I have done yesterday...

EDIT: I added the Code I used

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RomainL.
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1 Answers1

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It would have been better if you have shared your code as well as the error messages you got format these as such.

As far as I can understand, your problem is that you failed to make your cluster as default ids. For this you can use:

seurat_obj <- SetIdent(seurat_obj, id=seurat_obj@meta.data$column_of_interest).

The cluster identities are stored in the @meta.data slot of your object.

haci
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  • thank you for you answers, I don't know what I done yesterday, today it worked... do you know what I should do relative to the question? – RomainL. Jan 16 '20 at 08:23