now need to import Matrix::rowSums / Matrix::colSums to work with Del…

…ayedArrays for ..reasons?
RGLab · Apr 20, 2023 · 85ec051 · 85ec051
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commit 85ec051
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: MAST
 Type: Package
 Title: Model-based Analysis of Single Cell Transcriptomics
-Version: 1.25.1
-Date: 2022-11-29
+Version: 1.25.2
+Date: 2023-04-20
 Authors@R: c(person("Andrew", "McDavid", email = "Andrew_McDavid@urmc.rochester.edu", role = c("aut", "cre")),
             person("Greg", "Finak", email="gfinak@fredhutch.org", role='aut'),
             person("Masanao", "Yajima", email="myajima@fredhutch.org", role='aut'))
@@ -24,7 +24,8 @@ Imports:
     graphics,
     utils,
     SummarizedExperiment(>= 1.5.3),
-    progress
+    progress,
+    Matrix
 Depends:
     SingleCellExperiment (>= 1.2.0),
     R(>= 3.5)
@@ -49,7 +50,6 @@ Suggests:
     BiocStyle,
     scater,
     DelayedArray,
-    Matrix,
     HDF5Array,
     zinbwave,
     dplyr
@@ -88,7 +88,7 @@ Collate:
     'thresholdSCRNA.R'
     'zeroinf.R'
     'zlmHooks.R'
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 LazyData: true
 biocViews: GeneExpression, DifferentialExpression, GeneSetEnrichment,
     RNASeq, Transcriptomics, SingleCell

diff --git a/NAMESPACE b/NAMESPACE
@@ -72,6 +72,8 @@ import(SingleCellExperiment)
 import(abind)
 import(methods)
 import(stringr)
+importFrom(Matrix,colSums)
+importFrom(Matrix,rowSums)
 importFrom(SummarizedExperiment,"colData<-")
 importFrom(SummarizedExperiment,'assay<-')
 importFrom(SummarizedExperiment,'assayNames<-')

diff --git a/R/ebayes-helpers.R b/R/ebayes-helpers.R
@@ -65,6 +65,7 @@ getSSg_rNg <- function(assay_t, mm){
 ##' @param mm a model matrix, used when \code{model='H1'}.
 ##' @param truncate Genes with sample precisions exceeding this value are discarded when estimating the hyper parameters
 ##' @return \code{numeric} of length two, giving the hyperparameters in terms of a variance (\code{v}) and prior observations (\code{df}), inside a \code{structure}, with component \code{hess}, giving the Fisher Information of the hyperparameters.
+##' @importFrom Matrix colSums rowSums
 ebayes <- function(assay_t, ebayesControl, mm, truncate=Inf){
     ## Empirical bayes method
     defaultCtl <- list(method='MLE', model='H0')