Deleting cells from seurat object

I am attempting to delete PBMC cells from my seurat object. I would like to use the WhichCells function to identify the cells that contain these features. Here is my code:

WhichCells(OC_s, slot = 'counts', expression = PTPRC > 0 & CD3E > 0 & CD19 > 0 & MS4A1 > 0 
                   & CD3D > 0 & CD4 > 0 & CD8A > 0 & CD3E > 0 & NKG7 > 0 & IL7R > 0 
                   & CD19 > 0 & MS4A1 > 0 & CD79A > 0 & JCHAIN > 0 & IGHG3 > 0 
                   & IGKC > 0 & CD14 > 0 & LYZ > 0 & CD14 > 0 & CD68 > 0 & AIF1 > 0 
                   & C1QA  > 0 & CD1C > 0 & CD1A > 0 & CLEC9A > 0 & LILRA4 > 0 
                   & CXCR3 > 0 & CLEC9A > 0 & CD1C > 0 & CD1A > 0)

After this, I am hoping to filter out the cells above from my seurat object OC_s. I'm stuck at this point and I don't know if I'm doing this right. Can someone help me?

seurat

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written 2.5 years ago by odi •

once you identify the cells, you can subset the seurat object

colnames(pbmc3k) %>% head()

[1] "AAACATACAACCAC" "AAACATTGAGCTAC" "AAACATTGATCAGC" "AAACCGTGCTTCCG" "AAACCGTGTATGCG" "AAACGCACTGGTAC"

cells<- colnames(pbmc3k) %>% head()

pbmc3k[, cells] An object of class Seurat 13714 features across 6 samples within 1 assay

It may be better to cluster the cells and find the PBMC clusters and remove them that way.

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written 2.5 years ago by Ming Tommy Tang

Yes your suggestion was my original thought but unfortunately the way the experiment was done.... you had PBMC + tumor cells. So, they are mixed together and you are stuck trying to use the markers to identify the PBMC from tumor cells. Suggestions are appreciated.

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written 2.5 years ago by odi •

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