Merge branch 'master' into 39-errors-in-projectr-method-for-sparse-ma…

…trix-data

DESCRIPTION

@@ -2,7 +2,7 @@ Package: projectR
 Type: Package
 Title: Functions for the projection of weights from PCA, CoGAPS, NMF,
     correlation, and clustering
-Version: 1.19.2
+Version: 1.19.3
 Author: Gaurav Sharma, Charles Shin, Jared Slosberg, Loyal Goff, Genevieve Stein-O'Brien
 Authors@R: c(
     person("Gaurav", "Sharma", role = c("aut")),
@@ -15,6 +15,7 @@ Authors@R: c(
 Description: Functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering.
 License: GPL (==2)
 Imports:
+    SingleCellExperiment,
     methods,
     cluster,
     stats,
@@ -50,7 +51,7 @@ Suggests:
     SeuratObject
 LazyData: TRUE
 LazyDataCompression: gzip
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 VignetteBuilder: knitr
 biocViews: FunctionalPrediction, GeneRegulation, BiologicalQuestion, Software

NAMESPACE

@@ -21,6 +21,7 @@ exportClasses(correlateR)
 exportClasses(rotatoR)
 import(MatrixModels)
 import(RColorBrewer)
+import(SingleCellExperiment)
 import(cluster)
 import(dplyr)
 import(fgsea)

R/projectR.R

@@ -135,6 +135,7 @@ setMethod("projectR",signature(data="dgCMatrix",loadings="matrix"),function(
 
 #######################################################################################################################################
 #' @import limma
+#' @import SingleCellExperiment
 #' @importFrom NMF fcnnls
 #' @examples
 #' library("CoGAPS")

README.md

@@ -18,4 +18,4 @@ BiocManager::install("projectR")
 BiocManager::install("genesofeve/projectR")
 ```
 ## Getting Started
-We recommend going through the [vignette](https://www.bioconductor.org/packages/release/bioc/vignettes/projectR/inst/doc/projectR.pdf) and the [Bioinformatics article](https://academic.oup.com/bioinformatics/article/36/11/3592/5804979) to learn more about **projectR**.
+We recommend going through the [vignette](https://www.bioconductor.org/packages/release/bioc/vignettes/projectR/inst/doc/projectR.html) and the [Bioinformatics article](https://academic.oup.com/bioinformatics/article/36/11/3592/5804979) to learn more about **projectR**.