refactor readSCP()

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: scp
 Title: Mass Spectrometry-Based Single-Cell Proteomics Data Analysis
-Version: 1.13.2
+Version: 1.13.3
 Authors@R:
     c(person("Christophe", "Vanderaa",
               email = "[email protected]",

NAMESPACE

@@ -43,12 +43,10 @@ exportClasses(ScpModelFit)
 import(QFeatures)
 import(RColorBrewer)
 import(SingleCellExperiment)
-import(dplyr)
 import(ggplot2)
 importFrom(IHW,adj_pvalues)
 importFrom(IHW,ihw)
 importFrom(MsCoreUtils,normalize_matrix)
-importFrom(MultiAssayExperiment,ExperimentList)
 importFrom(MultiAssayExperiment,experiments)
 importFrom(QFeatures,aggregateFeatures)
 importFrom(QFeatures,readSummarizedExperiment)
@@ -59,10 +57,7 @@ importFrom(S4Vectors,List)
 importFrom(S4Vectors,endoapply)
 importFrom(S4Vectors,metadata)
 importFrom(SingleCellExperiment,"reducedDims<-")
-importFrom(SummarizedExperiment,"assay<-")
 importFrom(SummarizedExperiment,"assays<-")
-importFrom(SummarizedExperiment,"colData<-")
-importFrom(SummarizedExperiment,"rowData<-")
 importFrom(SummarizedExperiment,assay)
 importFrom(SummarizedExperiment,assayNames)
 importFrom(SummarizedExperiment,assays)
@@ -88,8 +83,6 @@ importFrom(stats,reformulate)
 importFrom(stats,sd)
 importFrom(stats,terms)
 importFrom(stats,var)
-importFrom(tidyr,pivot_wider)
 importFrom(utils,flush.console)
-importFrom(utils,read.csv)
 importFrom(utils,setTxtProgressBar)
 importFrom(utils,txtProgressBar)

NEWS.md

@@ -1,10 +1,15 @@
 # scp 1.13
 
+## scp 1.13.3
+
+- Refactor `readSCP()` and `readSCPFromDIANN()` to use new QFeatures
+  implementations.
+
 ## scp 1.13.2
 
-- fix: logFC and associated SE are now correctly computed
 - New *scplainer* workflow and citation
 - Add `addReducedDims()` (see #52)
+- fix: logFC and associated SE are now correctly computed
 
 ## scp 1.13.1