From a41296c74ff835be2426bec6ed5883fe2fc80837 Mon Sep 17 00:00:00 2001 From: Mike Kelly Date: Fri, 19 May 2023 10:10:17 -0400 Subject: [PATCH] Update convenience.R Xenium new blank unassigned assay With new version of Xenium output, the output matrix "Blank Codeword" was changed to "Unassigned Codeword". Suggesting change to allow import of this updated Xenium output. Not sure if a data version check needs to also be included. Thanks @aclark5 for finding this. --- R/convenience.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/convenience.R b/R/convenience.R index e2848908b..479a1af28 100644 --- a/R/convenience.R +++ b/R/convenience.R @@ -201,7 +201,7 @@ LoadXenium <- function(data.dir, fov = 'fov', assay = 'Xenium') { ) xenium.obj <- CreateSeuratObject(counts = data$matrix[["Gene Expression"]], assay = assay) - xenium.obj[["BlankCodeword"]] <- CreateAssayObject(counts = data$matrix[["Blank Codeword"]]) + xenium.obj[["BlankCodeword"]] <- CreateAssayObject(counts = data$matrix[["Unassigned Codeword"]]) xenium.obj[["ControlCodeword"]] <- CreateAssayObject(counts = data$matrix[["Negative Control Codeword"]]) xenium.obj[["ControlProbe"]] <- CreateAssayObject(counts = data$matrix[["Negative Control Probe"]])