From 93f609bf25cca2ba7b444be1f43faa0e818b91e7 Mon Sep 17 00:00:00 2001 From: Shivang Sharma <26456029+shivangsharma@users.noreply.github.com> Date: Tue, 22 Oct 2024 12:52:30 -0400 Subject: [PATCH] Update integrations.R Replace NormalizeData(), FindVariableFeatures() and ScaleData() with SCTransform() --- R/integrations.R | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/R/integrations.R b/R/integrations.R index b84b5bb..361d86c 100644 --- a/R/integrations.R +++ b/R/integrations.R @@ -72,9 +72,7 @@ seuratProcV3 <- function(count.matrix, vars.to.regress=NULL, verbose=TRUE, n.pcs message("Running Seurat v3 workflow") } so <- Seurat::CreateSeuratObject(counts = count.matrix) - so <- Seurat::NormalizeData(object = so, verbose = verbose) - so <- Seurat::FindVariableFeatures(object = so, verbose = verbose) - so <- Seurat::ScaleData(object = so, vars.to.regress = vars.to.regress, verbose = verbose) + so <- Seurat::SCTransform(object = so, vars.to.regress = vars.to.regress, verbose = verbose) so <- Seurat::RunPCA(object = so, npcs = n.pcs, verbose = verbose) if (cluster) { so <- Seurat::FindNeighbors(object = so, dims = 1:n.pcs, verbose = verbose)