Fix accessing counts

R/lun-estimate.R

@@ -25,7 +25,7 @@ lunEstimate <- function(counts, params = newLunParams()) {
 #' @rdname lunEstimate
 #' @export
 lunEstimate.SingleCellExperiment <- function(counts, params = newLunParams()) {
-    counts <- SingleCellExperiment::counts(counts)
+    counts <- SummarizedExperiment::assays(counts)$counts
     lunEstimate(counts, params)
 }
 

R/lun2-estimate.R

@@ -40,7 +40,7 @@ lun2Estimate.SingleCellExperiment <- function(counts, plates,
                                               params = newLun2Params(),
                                               min.size = 200, verbose = TRUE,
                                               BPPARAM = SerialParam()) {
-    counts <- SingleCellExperiment::counts(counts)
+    counts <- SummarizedExperiment::assays(counts)$counts
     lun2Estimate(counts, plates, params, min.size = min.size, verbose = verbose)
 }
 

R/scDD-estimate.R

@@ -40,7 +40,7 @@ scDDEstimate.SingleCellExperiment <- function(counts, conditions,
                                               params = newSCDDParams(),
                                               verbose = TRUE,
                                               BPPARAM = SerialParam()) {
-    counts <- SingleCellExperiment::counts(counts)
+    counts <- SummarizedExperiment::assays(counts)$counts
     scDDEstimate(counts, conditions, params, verbose, BPPARAM)
 }
 

R/simple-estimate.R

@@ -28,7 +28,7 @@ simpleEstimate <- function(counts, params = newSimpleParams()) {
 #' @export
 simpleEstimate.SingleCellExperiment <- function(counts,
                                                 params = newSimpleParams()) {
-    counts <- SingleCellExperiment::counts(counts)
+    counts <- SummarizedExperiment::assays(counts)$counts
     simpleEstimate(counts, params)
 }
 

R/splat-estimate.R

@@ -28,7 +28,7 @@ splatEstimate <- function(counts, params = newSplatParams()) {
 #' @export
 splatEstimate.SingleCellExperiment <- function(counts,
                                                params = newSplatParams()) {
-    counts <- SingleCellExperiment::counts(counts)
+    counts <- SummarizedExperiment::assays(counts)$counts
     splatEstimate(counts, params)
 }