@@ -29,8 +29,8 @@ Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,

 LinkingTo: Rcpp, RcppEigen

 License: MIT + file LICENSE

 Encoding: UTF-8

-LazyData: false

-RoxygenNote: 7.1.2

+LazyData: true

+RoxygenNote: 7.2.1

 BugReports: https://github.com/campbio/celda/issues

 biocViews: SingleCell, GeneExpression, Clustering, Sequencing, Bayesian, ImmunoOncology, DataImport

 NeedsCompilation: yes

@@ -1,5 +1,6 @@

 # celda v1.13.0 (2022-10-20)

 * Bug fixes related to cluster labels stored as factors and plotting

+* Updated sparse matrix conversion to work with Matrix v1.4-2

 # celda v1.12.0 (2022-04-30)

 * Update to match Bioconductor 3.15 release version

@@ -188,7 +188,7 @@ setMethod("celda_C",

         verbose = TRUE) {

         # Convert to sparse matrix

-        x <- methods::as(x, "dgCMatrix")

+        x <- methods::as(x, "CsparseMatrix")

         ls <- list()

         ls[[useAssay]] <- x

@@ -222,7 +222,7 @@ setMethod("celda_CG",

         verbose = TRUE) {

         # Convert to sparse matrix

-        x <- methods::as(x, "dgCMatrix")

+        x <- methods::as(x, "CsparseMatrix")

         ls <- list()

         ls[[useAssay]] <- x

@@ -172,7 +172,7 @@ setMethod("celda_G",

         verbose = TRUE) {

         # Convert to sparse matrix

-        x <- methods::as(x, "dgCMatrix")

+        x <- methods::as(x, "CsparseMatrix")

         ls <- list()

         ls[[useAssay]] <- x

@@ -493,11 +493,11 @@ setMethod(

         append = TRUE,

         verbose = verbose

       )

-      countsBat <- methods::as(countsBat, "dgCMatrix")

+      countsBat <- methods::as(countsBat, "CsparseMatrix")

     }

     if (!is.null(bgBat)) {

       if (!inherits(bgBat, "dgCMatrix")) {

-        bgBat <- methods::as(bgBat, "dgCMatrix")

+        bgBat <- methods::as(bgBat, "CsparseMatrix")

       }

     }