From a25de58403788fea4ebfa193969fd5133886987a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages@fredhutch.org>
Date: Fri, 18 Oct 2019 14:44:03 -0700
Subject: [PATCH] addPer*QC() functions were renamed in scater 1.13.27
---
DESCRIPTION | 6 +++---
R/compare.R | 8 ++++----
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index be5d289..b74ddbb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.9.9
-Date: 2019-10-16
+Version: 1.9.10
+Date: 2019-10-18
Authors@R:
c(person("Luke", "Zappia", role = c("aut", "cre"),
email = "luke@lazappi.id.au",
@@ -35,7 +35,7 @@ Imports:
matrixStats,
methods,
scales,
- scater (>= 1.13.11),
+ scater (>= 1.13.27),
stats,
SummarizedExperiment,
utils,
diff --git a/R/compare.R b/R/compare.R
index 3243d88..c210b28 100644
--- a/R/compare.R
+++ b/R/compare.R
@@ -79,8 +79,8 @@ compareSCEs <- function(sces, point.size = 0.1, point.alpha = 0.1,
sce <- sces[[name]]
rowData(sce)$Dataset <- name
colData(sce)$Dataset <- name
- sce <- scater::addQCPerCell(sce)
- sce <- scater::addQCPerFeature(sce)
+ sce <- scater::addPerCellQC(sce)
+ sce <- scater::addPerFeatureQC(sce)
cpm(sce) <- scater::calculateCPM(sce)
sce <- addFeatureStats(sce, "counts")
sce <- addFeatureStats(sce, "cpm")
@@ -358,8 +358,8 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
}
rowData(sce)$Dataset <- name
colData(sce)$Dataset <- name
- sce <- scater::addQCPerCell(sce)
- sce <- scater::addQCPerFeature(sce)
+ sce <- scater::addPerCellQC(sce)
+ sce <- scater::addPerFeatureQC(sce)
cpm(sce) <- scater::calculateCPM(sce)
sce <- addFeatureStats(sce, "counts")
sce <- addFeatureStats(sce, "cpm", log = TRUE)
--
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