@@ -168,10 +168,14 @@ setMethod("decontX", "SingleCellExperiment", function(x,

   countsBackground <- NULL

   if (!is.null(background)) {

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

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

-                                   logfile = logfile, verbose = verbose)

+    temp <- .checkBackground(x = x,

+                             background = background,

+                             bgBatch = bgBatch,

+                             logfile = logfile,

+                             verbose = verbose)

-    # TODO: Does bgBatch needs to be checked?

+    background <- temp$background

+    bgBatch <- temp$bgBatch

     if (is.null(bgAssayName)) {

       bgAssayName <- assayName

@@ -254,10 +258,14 @@ setMethod("decontX", "ANY", function(x,

   countsBackground <- NULL

   if (!is.null(background)) {

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

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

-                                   logfile = logfile, verbose = verbose)

+    temp <- .checkBackground(x = x,

+                             background = background,

+                             bgBatch = bgBatch,

+                             logfile = logfile,

+                             verbose = verbose)

-    # TODO: Does bgBatch needs to be checked?

+    background <- temp$background

+    bgBatch <- temp$bgBatch

   }

@@ -1388,8 +1396,10 @@ simulateContamination <- function(C = 300,

 }

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

+.checkBackground <- function(x, background, bgBatch,

+                             logfile = NULL, verbose = FALSE) {

   # Remove background barcodes that have already appeared in x

+  # If bgBatch param is supplied, also remove duplicate bgBatch

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

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

   } else {

@@ -1413,6 +1423,20 @@ simulateContamination <- function(C = 300,

       verbose = verbose

     )

     background <- background[, !(dupBarcode), drop = FALSE]

+    

+    if(!is.null(bgBatch)){

+      if (length(bgBatch) != length(dupBarcode)) {

+        stop(

+          "Length of bgBatch must be equal to the number of columns",

+          "of background matrix."

+          )

+      }

+      bgBatch <- bgBatch[!(dupBarcode)]

+    }

   }

-  return(background)

+  

+  re = list(background = background,

+            bgBatch = bgBatch)

+  

+  return(re)

 }