diff --git a/inst/templates/singlecell/pre-process-w-cellranger.md b/inst/templates/singlecell/pre-process-w-cellranger.md index b5f7af5..0945f97 100644 --- a/inst/templates/singlecell/pre-process-w-cellranger.md +++ b/inst/templates/singlecell/pre-process-w-cellranger.md @@ -211,7 +211,7 @@ for (i in 3:length(seurat_ID)) { seurat_merge <- merge(x = get(seurat_ID[1]), y = u, - add.cell.ids = all_samples, + add.cell.ids = samples, project = "my_scRNA_project") ``` @@ -262,6 +262,8 @@ seurat_merge$Log10GenesPerUMI <- log10(seurat_merge$nFeature_RNA) / log10(seurat # Import experimental metadata metaexp <- read.csv("/path/to/experimental/metadata/meta.csv") +metadata <- seurat_merge@meta.data +metadata$barcode <- rownames(metadata) # Check matching of IDs all(metaexp$sample %in% metadata$orig.ident)