@@ -84,6 +84,13 @@ runDecontX <- function(inSCE,

   message(paste0(date(), " ... Running 'DecontX'"))

+  rm.ix <- which(colSums(assay(inSCE, useAssay)) == 0)

+  if(length(rm.ix) > 0){

+    inSCEOrig <- inSCE

+    inSCE <- inSCE[,-rm.ix]

+    sample <- sample[-rm.ix]

+  }

+

   inSCE <- celda::decontX(x = inSCE,

                           batch = sample,

                           assayName = useAssay,

@@ -101,6 +108,9 @@ runDecontX <- function(inSCE,

   #argsList <- argsList[!names(argsList) %in% ("...")]

+  if(length(rm.ix) > 0){

+    inSCE <- mergeSCEColData(inSCE1 = inSCEOrig, inSCE2 = inSCE)

+  }

   inSCE@metadata$runDecontX <- argsList[-1]

   inSCE@metadata$runDecontX$packageVersion <- utils::packageDescription("celda")$Version

@@ -1,16 +1,16 @@

 #' @title Merging colData from two singleCellExperiment objects

-#' @description Merges colData of the singleCellExperiment objects 

-#'  obtained from the same dataset which contain differing colData. 

-#'  (i.e. raw data and filtered data)  

+#' @description Merges colData of the singleCellExperiment objects

+#'  obtained from the same dataset which contain differing colData.

+#'  (i.e. raw data and filtered data)

 #' @param inSCE1 Input SingleCellExperiment object. The function will output this

 #'  singleCellExperiment object with a combined colData from inSCE1 and inSCE2.

 #' @param inSCE2 Input SingleCellExperiment object. colData from this object

 #'  will be merged with colData from inSCE1 and loaded into inSCE1.

-#' @param id1 Character vector. Column in colData of inSCE1 that will be 

-#'  used to combine inSCE1 and inSCE2. Default "column_name" 

+#' @param id1 Character vector. Column in colData of inSCE1 that will be

+#'  used to combine inSCE1 and inSCE2. Default "column_name"

 #' @param id2 Character vector. Column in colData of inSCE2 that will be

 #'  used to combine inSCE1 and inSCE2. Default "column_name"

-#' @return SingleCellExperiment object containing combined colData from  

+#' @return SingleCellExperiment object containing combined colData from

 #'  both singleCellExperiment for samples in inSCE1.

 #' @examples

 #' sce1 <- importCellRanger(

@@ -22,48 +22,70 @@

 #' sce2 <- sce

 #' sce <- mergeSCEColData(inSCE1 = sce1, inSCE2 = sce2, id1 = "column_name", id2 = "column_name")

 #' @export

-mergeSCEColData <- function(inSCE1, inSCE2, id1 = "column_name", id2 = "column_name"){

-    not.in.sce1 <- c(setdiff(names(SummarizedExperiment::colData(inSCE2)),

-      names(SummarizedExperiment::colData(inSCE1))),id2)

-    not.in.sce1 <- not.in.sce1[!is.null(not.in.sce1)]

+mergeSCEColData <- function(inSCE1, inSCE2, id1 = "column_name", id2 = "column_name") {

+  # For default case & column_name not in colData

+  if (id1 == "column_name" && "column_name" %in%

+    names(SummarizedExperiment::colData(inSCE1))) {

+    columnNameColExist1 <- TRUE

+  } else {

+    columnNameColExist1 <- FALSE

+    SummarizedExperiment::colData(inSCE1)$column_name <- colnames(inSCE1)

+  }

+

+  if (id2 == "column_name" && "column_name" %in%

+    names(SummarizedExperiment::colData(inSCE2))) {

+    columnNameColExist2 <- TRUE

+  } else {

+    columnNameColExist2 <- FALSE

+    SummarizedExperiment::colData(inSCE2)$column_name <- colnames(inSCE2)

+  }

+  not.in.sce1 <- c(setdiff(

+    names(SummarizedExperiment::colData(inSCE2)),

+    names(SummarizedExperiment::colData(inSCE1))

+  ), id2)

+  not.in.sce1 <- not.in.sce1[!is.null(not.in.sce1)]

-    coldata.not.in.sce1 <- SummarizedExperiment::colData(inSCE2)[,c(not.in.sce1),

-      drop = FALSE]

+  coldata.not.in.sce1 <- SummarizedExperiment::colData(inSCE2)[, c(not.in.sce1),

+    drop = FALSE

+  ]

-    coldata.sce1 <- SummarizedExperiment::colData(inSCE1)

+  coldata.sce1 <- SummarizedExperiment::colData(inSCE1)

-    if(is.null(id1) | is.null(id2)){

-        if(is.null(rownames(coldata.not.in.sce1))){

-            stop("Unable to match between singleCellExperiment objects.

+  if (is.null(id1) | is.null(id2)) {

+    if (is.null(rownames(coldata.not.in.sce1))) {

+      stop("Unable to match between singleCellExperiment objects.

               Please define id1/id2 within the function,

               or assign a column name for the singleCellExperiment object.")

-        }else{

-            coldata.not.in.sce1$cell <- rownames(coldata.not.in.sce1)

-            coldata.sce1$cell <- rownames(SummarizedExperiment::colData(inSCE1))

-            id1 <- "cell"

-            id2 <- "cell"

-            placeholder = TRUE

-        }

-    }else{

-        placeholder <- FALSE

+    } else {

+      coldata.not.in.sce1$cell <- rownames(coldata.not.in.sce1)

+      coldata.sce1$cell <- rownames(SummarizedExperiment::colData(inSCE1))

+      id1 <- "cell"

+      id2 <- "cell"

+      placeholder <- TRUE

     }

+  } else {

+    placeholder <- FALSE

+  }

-    coldata.merge <- base::merge(coldata.sce1,

-        coldata.not.in.sce1,

-        all.x = TRUE,

-        sort = FALSE,

-        by.x = id1,

-        by.y = id2)

+  coldata.merge <- base::merge(coldata.sce1,

+    coldata.not.in.sce1,

+    all.x = TRUE,

+    sort = FALSE,

+    by.x = id1,

+    by.y = id2

+  )

-    coldata.merge <- coldata.merge[match(colnames(SingleCellExperiment::counts(inSCE1)),

-        coldata.merge[,id1]),]

+  coldata.merge <- coldata.merge[match(

+    colnames(SingleCellExperiment::counts(inSCE1)),

+    coldata.merge[, id1]

+  ), ]

-    rownames(coldata.merge) <- coldata.merge[,id1]

+  rownames(coldata.merge) <- coldata.merge[, id1]

-    if(placeholder == TRUE){

-    	  coldata.merge[,id1] <- NULL

-    }

+  if (placeholder == TRUE) {

+    coldata.merge[, id1] <- NULL

+  }

-    SummarizedExperiment::colData(inSCE1) <- S4Vectors::DataFrame(coldata.merge)

-    return(inSCE1)

+  SummarizedExperiment::colData(inSCE1) <- S4Vectors::DataFrame(coldata.merge)

+  return(inSCE1)

 }

@@ -13,9 +13,9 @@

 #                               BSPARAM=BSPARAM,

 #                               BPPARAM=BPPARAM

 #                               ) {

-# 

+#

 #   cell.matrix <- .convertToMatrix(cell.matrix)

-# 

+#

 #   scores <- matrix(scran::doubletCells(cell.matrix, k = k,

 #                                        niters = nIters,

 #                                        size.factors.norm = NULL,

@@ -32,11 +32,11 @@

 #                                        ), ncol=1)

 #   scores <- cbind(scores,log10(scores[,1]+1))

 #   colnames(scores) <- c("scran_doubletCells_score", "scran_doubletCells_score_log10")

-# 

-# 

+#

+#

 #   return(scores)

 # }

-# 

+#

 #' @title Detect doublet cells using \link[scDblFinder]{scDblFinder}.

 #' @description A wrapper function for \link[scDblFinder]{scDblFinder}. Identify

@@ -109,7 +109,13 @@ runDoubletCells <- function(inSCE,

   ## Loop through each sample and run barcodeRank

   #samples <- unique(sample)

-  

+

+  rm.ix <- which(colSums(assay(inSCE, useAssay)) == 0)

+  if(length(rm.ix) > 0){

+    inSCEOrig <- inSCE

+    inSCE <- inSCE[,-rm.ix]

+    sample <- sample[-rm.ix]

+  }

   inSCE <- withr::with_seed(seed,

                             scDblFinder::scDblFinder(sce = inSCE,

                             samples = sample,

@@ -117,16 +123,19 @@ runDoubletCells <- function(inSCE,

                             k = nNeighbors,

                             verbose = FALSE

                             ))

+  if(length(rm.ix) > 0){

+    inSCE <- mergeSCEColData(inSCE1 = inSCEOrig, inSCE2 = inSCE)

+  }

   names(SummarizedExperiment::colData(inSCE)) <- gsub(pattern = "scDblFinder\\.",

                                                       "scran_doubletCells_",

                                                       names(SummarizedExperiment::colData(inSCE)))

-  

+

   # for (i in seq_len(length(samples))) {

   #   sceSampleInd <- sample == samples[i]

   #   sceSample <- inSCE[, sceSampleInd]

-  # 

+  #

   #   mat <- SummarizedExperiment::assay(sceSample, i = useAssay)

-  # 

+  #

   #   result <- withr::with_seed(seed,

   #             .runDoubletCells(cell.matrix = mat,

   #                              k = nNeighbors,

@@ -143,7 +152,7 @@ runDoubletCells <- function(inSCE,

   #                              BSPARAM=BSPARAM,

   #                              BPPARAM=BPPARAM

   #                              ))

-  # 

+  #

   #   output[sceSampleInd, ] <- result

   # }

@@ -13,19 +13,19 @@ singleCellExperiment object with a combined colData from inSCE1 and inSCE2.}

 \item{inSCE2}{Input SingleCellExperiment object. colData from this object

 will be merged with colData from inSCE1 and loaded into inSCE1.}

-\item{id1}{Character vector. Column in colData of inSCE1 that will be 

+\item{id1}{Character vector. Column in colData of inSCE1 that will be

 used to combine inSCE1 and inSCE2. Default "column_name"}

 \item{id2}{Character vector. Column in colData of inSCE2 that will be

 used to combine inSCE1 and inSCE2. Default "column_name"}

 }

 \value{

-SingleCellExperiment object containing combined colData from  

+SingleCellExperiment object containing combined colData from

  both singleCellExperiment for samples in inSCE1.

 }

 \description{

-Merges colData of the singleCellExperiment objects 

- obtained from the same dataset which contain differing colData. 

+Merges colData of the singleCellExperiment objects

+ obtained from the same dataset which contain differing colData.

  (i.e. raw data and filtered data)

 }

 \examples{