@@ -487,6 +487,17 @@ setMethod(

         )

       )

     }

+

+    ## Try to convert class of new matrix to class of original matrix

+    

+    .logMessages(

+      date(),

+      ".. Calculating final decontaminated matrix",

+      logfile = logfile,

+      append = TRUE,

+      verbose = verbose

+    )

+

     estRmat.temp <- calculateNativeMatrix(

       counts = countsBat,

       theta = res$theta,

@@ -495,6 +506,8 @@ setMethod(

       z = as.integer(res$z),

       pseudocount = 1e-20

     )

+

+    # This part needs to be optimized

     estRmat[seq(nrow(counts)), which(batch == bat)] <- estRmat.temp

     dimnames(estRmat) <- list(geneNames, allCellNames)

@@ -528,19 +541,17 @@ setMethod(

     "z" = returnZ

   )

-  ## Try to convert class of new matrix to class of original matrix

-  if (inherits(counts, "dgCMatrix")) {

+

+  if (inherits(counts, c("DelayedMatrix", "DelayedArray"))) {

+

     .logMessages(

       date(),

-      ".. Finalizing decontaminated matrix",

+      ".. Converting decontaminated matrix to ", class(counts),

       logfile = logfile,

       append = TRUE,

       verbose = verbose

     )

-  }

-

-  if (inherits(counts, c("DelayedMatrix", "DelayedArray"))) {

-

+    

     ## Determine class of seed in DelayedArray

     seed.class <- unique(DelayedArray::seedApply(counts, class))[[1]]

     if (seed.class == "HDF5ArraySeed") {