responses to initial review

AlexsLemonade · Dec 6, 2024 · 70fba8f · 70fba8f
1 parent 248c1c1
commit 70fba8f
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Showing 3 changed files with 6 additions and 9 deletions.
diff --git a/R/make-seurat.R b/R/make-seurat.R
@@ -66,11 +66,11 @@ sce_to_seurat <- function(
   reducedDims(sce) <- reducedDims(sce) |>
     purrr::map(\(mat) {
       # insert underscore between letters and numbers in axis labels
-      names <- gsub("([A-Za-z]+)([0-9]+)", "\\1_\\2", colnames(mat)) |>
+      rd_names <- gsub("([A-Za-z]+)([0-9]+)", "\\1_\\2", colnames(mat)) |>
         tolower()
-      colnames(mat) <- names
+      colnames(mat) <- rd_names
       if (!is.null(attr(mat, "rotation"))) {
-        colnames(attr(mat, "rotation")) <- names
+        colnames(attr(mat, "rotation")) <- rd_names
       }
       return(mat)
     })
@@ -93,9 +93,6 @@ sce_to_seurat <- function(
     sce_meta$highly_variable_genes <- NULL # remove from metadata to avoid redundancy
   }
 
-  # move rotation to feature.loadings
-
-
   # convert and set functions depending on assay version requested
   if (seurat_assay_version == "v5") {
     create_seurat_assay <- SeuratObject::CreateAssay5Object

diff --git a/man/sce_to_seurat.Rd b/man/sce_to_seurat.Rd
diff --git a/man/sum_duplicate_genes.Rd b/man/sum_duplicate_genes.Rd