nf Convert10Xfolders NormalizeData

R/Seurat.Utils.Metadata.R

@@ -526,18 +526,18 @@ addMetaFraction <- function(
     layer = "data",
     gene.set = FALSE,
     verbose = TRUE) {
+  #
+  message("Should rather use the default `Seurat::PercentageFeatureSet`")
+  message("Assay: ", assay)
+  message("Layer: ", layer)
+
   stopifnot(
     is(obj, "Seurat"),
     is.character(col.name), is.character(assay), is.character(layer),
     is.logical(gene.set), is.logical(verbose),
     assay %in% Assays(obj), layer %in% Layers(obj)
   )
 
-  message("Should rather use the default `Seurat::PercentageFeatureSet`")
-  message("Assay: ", assay)
-  message("Layer: ", layer)
-
-
   stopif(condition = isFALSE(gene.set) && isFALSE(gene.symbol.pattern), "Either gene.set OR gene.symbol.pattern has to be defined (!= FALSE).")
   if (!isFALSE(gene.set) && !isFALSE(gene.symbol.pattern) && verbose) print("Both gene.set AND gene.symbol.pattern are defined. Only using gene.set.")
 

R/Seurat.Utils.R

@@ -4421,6 +4421,7 @@ PlotUpdateStats <- function(mat = UpdateStatMat, column.names = c("Updated (%)",
 #' @param suffix A character string specifying the suffix of the files saved.
 #' @param min.cells An integer value specifying the minimum number of cells. Default: 5.
 #' @param min.features An integer value specifying the minimum number of features. Default: 200.
+#' @param normalize_data Add normalized "data" layer?. Default: `TRUE`.
 #' @param updateHGNC A logical value indicating whether to update the HGNC. Default: `TRUE`.
 #' @param save Save .qs object? Default: `TRUE`.
 #' @param ShowStats A logical value indicating whether to show statistics. Default: `TRUE`.
@@ -4441,6 +4442,7 @@ Convert10Xfolders <- function(
     suffix = strsplit(folderPattern, "_")[[1]][1],
     depth = 4,
     min.cells = 5, min.features = 200,
+    normalize_data = TRUE,
     updateHGNC = TRUE, ShowStats = TRUE,
     writeCBCtable = TRUE,
     nthreads = .getNrCores(),
@@ -4499,6 +4501,9 @@ Convert10Xfolders <- function(
     # update --- --- ---
     if (updateHGNC) seu <- UpdateGenesSeurat(seu, EnforceUnique = TRUE, ShowStats = TRUE)
 
+    # NormalizeData --- --- ---
+    if (normalize_data) seu <- NormalizeData(seu, normalization.method = "LogNormalize", scale.factor = 10000,  verbose = TRUE)
+
     # write out --- --- ---
     if (save) qs::qsave(x = seu, file = f.path.out, nthreads = nthreads, preset = preset)