@@ -162,22 +162,9 @@ setMethod("decontX", "SingleCellExperiment", function(x,

                                                       verbose = TRUE) {

   countsBackground <- NULL

   if (!is.null(background)) {

-    # Remove background barcodes that have already appeared in x

-    dupBarcode <- background$Barcode %in% x$Barcode

-

-    if (any(dupBarcode)) {

-      .logMessages(

-        sum(dupBarcode),

-        " columns in background removed as they are found in filtered matrix",

-        logfile = logfile,

-        append = TRUE,

-        verbose = verbose

-      )

-    }

-

-    background <- background[, !(dupBarcode)]

-

-

+    # Remove cells with the same ID between x and the background matrix

+    background <- .checkBackground(x = x, background = background,

+                                   logfile = logfile, verbose = verbose)

     if (is.null(bgAssayName)) {

       bgAssayName <- assayName

     }

@@ -256,20 +243,9 @@ setMethod("decontX", "ANY", function(x,

   countsBackground <- NULL

   if (!is.null(background)) {

-    # Remove background barcodes that have already appeared in x

-    dupBarcode <- colnames(background) %in% colnames(x)

-

-    if (any(dupBarcode)) {

-      .logMessages(

-        sum(dupBarcode),

-        " columns in background removed as they are found in filtered matrix",

-        logfile = logfile,

-        append = TRUE,

-        verbose = verbose

-      )

-    }

-

-    countsBackground <- background[, !(dupBarcode)]

+    # Remove cells with the same ID between x and the background matrix

+    background <- .checkBackground(x = x, background = background,

+                                   logfile = logfile, verbose = verbose)

   }

   .decontX(

@@ -1368,3 +1344,31 @@ simulateContamination <- function(C = 300,

     )

   )

 }

+

+

+.checkBackground <- function(x, background, logfile = NULL, verbose = FALSE) {

+  # Remove background barcodes that have already appeared in x

+  if(!is.null(colnames(background))) {

+    dupBarcode <- colnames(background) %in% colnames(x)

+  } else {

+    dupBarcode <- FALSE

+    warning("No column names were found for the 'background' matrix. ",

+            "No checking was performed between the ids in the 'backgroud' ",

+            "matrix and 'x'.",

+            " Please ensure that no true cells are included in the background ",

+            "matrix. Otherwise, results will be incorrect.")

+  }

+  

+  if (any(dupBarcode)) {

+    .logMessages(

+      sum(dupBarcode),

+      " columns in the background matrix were removed as they were found in",

+      " the filtered matrix.",

+      logfile = logfile,

+      append = TRUE,

+      verbose = verbose

+    )

+    background <- background[, !(dupBarcode)]

+  }

+  return(background)

+}