Follow up #8260 - reclustering using SCT - v5

[anaccsilva]

Hello, I would like to follow up on issue #8260. I have tried to use the Findsubcluster, but once I could not find any example, I preferred not to move forward with it. Instead, I have tried the second option to re-run the entire integration, but I am not sure if I did it correctly.

`#subset object and rerun integration obj2= subset(obj1, idents = c("cluster_3")) DefaultAssay(obj2) <- "SCT"

obj2<- RunPCA(obj2) obj2 <- RunUMAP(obj2, dims = 1:30) DimPlot(obj2, reduction = "umap", group.by = c("disease", "patients"))

obj2 <- IntegrateLayers(object = obj2, method = CCAIntegration, normalization.method = "SCT", verbose = T) obj2<- FindNeighbors(obj2, reduction = "integrated.dr", dims = 1:30) obj2 <- FindClusters(obj2, resolution = 0.2)

obj2 <- RunUMAP(obj2, dims = 1:30, reduction = "integrated.dr") DimPlot(obj2, reduction = "umap", group.by = c("disease", "patients"))`

Would this be correct? After that, to find markers, I should use recorrect_umi = FALSE, correct?

Thank you for the help. Ana