From a83516903133c89fc850a3295d79d7c775d94106 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Thu, 7 Sep 2017 15:56:00 +1000
Subject: [PATCH] Fix accessing counts
---
R/{SCESet-functions.R => SCE-functions.R} | 0
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, 5 insertions(+), 5 deletions(-)
rename R/{SCESet-functions.R => SCE-functions.R} (100%)
diff --git a/R/SCESet-functions.R b/R/SCE-functions.R
similarity index 100%
rename from R/SCESet-functions.R
rename to R/SCE-functions.R
diff --git a/R/lun-estimate.R b/R/lun-estimate.R
index 8970079..afa303f 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 <- SingleCellExperiment::counts(counts)
+ counts <- SummarizedExperiment::assays(counts)$counts
lunEstimate(counts, params)
}
diff --git a/R/lun2-estimate.R b/R/lun2-estimate.R
index b4786b4..33a0d65 100644
--- a/R/lun2-estimate.R
+++ b/R/lun2-estimate.R
@@ -40,7 +40,7 @@ lun2Estimate.SingleCellExperiment <- function(counts, plates,
params = newLun2Params(),
min.size = 200, verbose = TRUE,
BPPARAM = SerialParam()) {
- counts <- SingleCellExperiment::counts(counts)
+ counts <- SummarizedExperiment::assays(counts)$counts
lun2Estimate(counts, plates, params, min.size = min.size, verbose = verbose)
}
diff --git a/R/scDD-estimate.R b/R/scDD-estimate.R
index 5f52157..5626394 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 <- SingleCellExperiment::counts(counts)
+ counts <- SummarizedExperiment::assays(counts)$counts
scDDEstimate(counts, conditions, params, verbose, BPPARAM)
}
diff --git a/R/simple-estimate.R b/R/simple-estimate.R
index 793be3c..4f09ed4 100644
--- a/R/simple-estimate.R
+++ b/R/simple-estimate.R
@@ -28,7 +28,7 @@ simpleEstimate <- function(counts, params = newSimpleParams()) {
#' @export
simpleEstimate.SingleCellExperiment <- function(counts,
params = newSimpleParams()) {
- counts <- SingleCellExperiment::counts(counts)
+ counts <- SummarizedExperiment::assays(counts)$counts
simpleEstimate(counts, params)
}
diff --git a/R/splat-estimate.R b/R/splat-estimate.R
index b1523f2..496edf1 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 <- SingleCellExperiment::counts(counts)
+ counts <- SummarizedExperiment::assays(counts)$counts
splatEstimate(counts, params)
}
--
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