From 779ff32ffb52bda64ff138895f627084a2b7d5d6 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Fri, 8 Sep 2017 11:51:33 +1000
Subject: [PATCH] Switch to BiocGenerics::counts
---
R/SCE-functions.R | 6 +++---
R/lun-estimate.R | 2 +-
R/lun2-estimate.R | 2 +-
R/scDD-estimate.R | 2 +-
R/simple-estimate.R | 2 +-
R/splat-estimate.R | 2 +-
6 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/R/SCE-functions.R b/R/SCE-functions.R
index a4b97d8..34bc7ad 100644
--- a/R/SCE-functions.R
+++ b/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)$tpm
+ values = SingleCellExperiment::tpm(sce)
suffix <- "TPM"
},
fpkm = {
diff --git a/R/lun-estimate.R b/R/lun-estimate.R
index afa303f..3191a5d 100644
--- a/R/lun-estimate.R
+++ b/R/lun-estimate.R
@@ -25,7 +25,7 @@ lunEstimate <- function(counts, params = newLunParams()) {
#' @rdname lunEstimate
#' @export
lunEstimate.SingleCellExperiment <- function(counts, params = newLunParams()) {
- counts <- SummarizedExperiment::assays(counts)$counts
+ counts <- BiocGenerics::counts(counts)
lunEstimate(counts, params)
}
diff --git a/R/lun2-estimate.R b/R/lun2-estimate.R
index 33a0d65..df51b84 100644
--- a/R/lun2-estimate.R
+++ b/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)$counts
+ counts <- BiocGenerics::counts(counts)
lun2Estimate(counts, plates, params, min.size = min.size, verbose = verbose)
}
diff --git a/R/scDD-estimate.R b/R/scDD-estimate.R
index 5626394..7253c61 100644
--- a/R/scDD-estimate.R
+++ b/R/scDD-estimate.R
@@ -40,7 +40,7 @@ scDDEstimate.SingleCellExperiment <- function(counts, conditions,
params = newSCDDParams(),
verbose = TRUE,
BPPARAM = SerialParam()) {
- counts <- SummarizedExperiment::assays(counts)$counts
+ counts <- BiocGenerics::counts(counts)
scDDEstimate(counts, conditions, params, verbose, BPPARAM)
}
diff --git a/R/simple-estimate.R b/R/simple-estimate.R
index 4f09ed4..3a50a41 100644
--- a/R/simple-estimate.R
+++ b/R/simple-estimate.R
@@ -28,7 +28,7 @@ simpleEstimate <- function(counts, params = newSimpleParams()) {
#' @export
simpleEstimate.SingleCellExperiment <- function(counts,
params = newSimpleParams()) {
- counts <- SummarizedExperiment::assays(counts)$counts
+ counts <- BiocGenerics::counts(counts)
simpleEstimate(counts, params)
}
diff --git a/R/splat-estimate.R b/R/splat-estimate.R
index 496edf1..ead3c49 100644
--- a/R/splat-estimate.R
+++ b/R/splat-estimate.R
@@ -28,7 +28,7 @@ splatEstimate <- function(counts, params = newSplatParams()) {
#' @export
splatEstimate.SingleCellExperiment <- function(counts,
params = newSplatParams()) {
- counts <- SummarizedExperiment::assays(counts)$counts
+ counts <- BiocGenerics::counts(counts)
splatEstimate(counts, params)
}
--
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