Merge pull request #455 from tuonglab/fix-shuffling

fix shuffling of cell barcodes in SingleCellExperiment object
BorchLab · Dec 10, 2024 · b1fe3f1 · b1fe3f1
2 parents 08e80ab + 4a2e080
commit b1fe3f1
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/R/combineExpression.R b/R/combineExpression.R
@@ -201,11 +201,11 @@ combineExpression <- function(input.data,
 
       combined_col_names <- unique(c(colnames(colData(sc.data)), colnames(PreMeta)))
       full_data <- merge(colData(sc.data), PreMeta[rownames, , drop = FALSE], by = "row.names", all.x = TRUE)
+      # at this point, the rows in full_data are shuffled. match back with the original colData
+      full_data <- full_data[match(rownames, full_data[,1]), ]
       rownames(full_data) <- full_data[, 1]
       full_data  <- full_data[, -1]
-      colData(sc.data) <- DataFrame(full_data[, combined_col_names])
-
-      rownames(colData(sc.data)) <- rownames  
+      colData(sc.data) <- DataFrame(full_data[, combined_col_names])  
     }
     if (filterNA) { 
       sc.data <- .filteringNA(sc.data)