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 :)