Hello,

I've combined 3 seurat files in order to do an integrated analysis and everything is working fine, but I would like to extract some cells for subsequent analysis. As the dimplot is now, the clusters consist of cells from all of my conditions so I can not seem to do the usual approach which would be something like :

    Cluster.1.8.12.only <- subset(x = seuratA, idents = c('1','8', '12'))
if for example I wanted clusters 1,8 and 12. 

Does anyone know how I would modify the above to for example, get clusters 1, 8 and 12 but of only the condition I'm interested in? for simplicity sake lets assume the conditions are labelled A, B and C and are in an integrated seurat called ABC.combined.

Thank you for your help :)
I'd probably just subset again. Same approach, just using the metadata column using your condition.

    Cluster.1.8.12.cond <- subset(x = Cluster.1.8.12.only, subset = your_condition_column == "condition_of_interest")