Switch to BiocGenerics::counts

R/SCE-functions.R

@@ -33,15 +33,15 @@ addFeatureStats <- function(sce, value = c("counts", "cpm", "tpm", "fpkm"),
 
     switch(value,
            counts = {
-               values = SummarizedExperiment::assays(sce)$counts
+               values = BiocGenerics::counts(sce)
                suffix <- "Counts"
            },
            cpm = {
-               values = SummarizedExperiment::assays(sce)$cpm
+               values = SingleCellExperiment::cpm(sce)
                suffix <- "CPM"
            },
            tpm = {
-               values = SummarizedExperiment::assays(sce)$tpm
+               values = SingleCellExperiment::tpm(sce)
                suffix <- "TPM"
            },
            fpkm = {

R/lun-estimate.R

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