Is there a way to import gene list into Seurat to define cell type? The default cell types in Seurat is not enough for our research. For example, we want to mark a subtype of B cells in Seurat, but seems like Seurat only have general B cell, I'm planning to download gene list from Genomic Cytometry, and then import the gene list into Seurat and then Seurat define cell types in the cluster based on the gene list I import. Does Seurat support this function?
Seurat does not define cell types by name. It clusters and assigns each cell to a cluster, from 0 to X. If your data has the cell type (e.g. B,T, Mast cells) it means that someone annotate the clusters so that they have a biological meaning.
You can assign different names to the clusters by using the
sampleID cellType cell1 B cell2 B cell3 T cell4 T newMeta <- oldMEta newMeta$origType <- newMeta$cellType newMeta$cellType <- c("B1","B","Treg","Tkill") object <- AddMetaData(object, newMeta)
The new metadata should look like
sampleID origType cellType cell1 B B1 cell2 B B cell3 T Treg cell4 T Tkill
You can then swap the labels using
SetAllIdent(object = test, id = "cellType"). Your tSNE or uMAp, will now show the new cell types.
You can use scID with your gene list to find the cells that match your gene list. You can then find which cluster in Seurat have these cells.
Maybe you can try
FeaturePlot() and see if some of your B cells are different. After plotting this on
GenePlot(), perhaps you can set a cutoff, then assign identities.
Alternatively, use your B cell gene list in
RunPCA(object, pc.genes = yourgenelist) instead of the usual variable genes. You can also subset B cells first with
SubsetData(), and run the above.