@@ -154,6 +154,7 @@ setMethod("decontX", "SingleCellExperiment", function(x,

                                                       batch = NULL,

                                                       background = NULL,

                                                       bgAssayName = NULL,

+                                                      bgBatch = NULL,

                                                       maxIter = 500,

                                                       delta = c(10, 10),

                                                       estimateDelta = TRUE,

@@ -182,6 +183,7 @@ setMethod("decontX", "SingleCellExperiment", function(x,

     z = z,

     batch = batch,

     countsBackground = countsBackground,

+    batchBackground = bgBatch,

     maxIter = maxIter,

     convergence = convergence,

     iterLogLik = iterLogLik,

@@ -234,6 +236,7 @@ setMethod("decontX", "ANY", function(x,

                                      z = NULL,

                                      batch = NULL,

                                      background = NULL,

+                                     bgBatch = NULL,

                                      maxIter = 500,

                                      delta = c(10, 10),

                                      estimateDelta = TRUE,

@@ -257,6 +260,7 @@ setMethod("decontX", "ANY", function(x,

     z = z,

     batch = batch,

     countsBackground = countsBackground,

+    batchBackground = bgBatch,

     maxIter = maxIter,

     convergence = convergence,

     iterLogLik = iterLogLik,

@@ -339,6 +343,7 @@ setMethod(

                      z = NULL,

                      batch = NULL,

                      countsBackground = NULL,

+                     batchBackground = NULL,

                      maxIter = 200,

                      convergence = 0.001,

                      iterLogLik = 10,

@@ -369,6 +374,7 @@ setMethod(

   runParams <- list(

     z = z,

     batch = batch,

+    batchBackground = batchBackground,

     maxIter = maxIter,

     delta = delta,

     estimateDelta = estimateDelta,

@@ -398,6 +404,7 @@ setMethod(

   ## Generate batch labels if none were supplied

   if (is.null(batch)) {

     batch <- rep("all_cells", nC)

+    batchBackground <- rep("all_cells", ncol(countsBackground))

   }

   runParams$batch <- batch

   batchIndex <- unique(batch)