Merge pull request #294 from stemangiola/fix-dependency-keep-variable

use Matrix library for sparse counts
stemangiola · Sep 18, 2023 · 749ce37 · 749ce37
2 parents be98005 + 6386415
commit 749ce37
Show file tree

Hide file tree

Showing 3 changed files with 5 additions and 2 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -35,7 +35,8 @@ Imports:
     GenomicRanges,
     methods,
     S4Vectors,
-    crayon
+    crayon,
+    Matrix
 Suggests:
     BiocStyle,
     testthat,

diff --git a/NAMESPACE b/NAMESPACE
@@ -83,6 +83,7 @@ import(preprocessCore)
 import(readr)
 import(tibble)
 importFrom(GenomicRanges,makeGRangesListFromDataFrame)
+importFrom(Matrix,colSums)
 importFrom(S4Vectors,metadata)
 importFrom(SummarizedExperiment,SummarizedExperiment)
 importFrom(SummarizedExperiment,assays)

diff --git a/R/methods_SE.R b/R/methods_SE.R
@@ -1589,6 +1589,7 @@ setMethod("keep_variable",
 #'
 #' @importFrom purrr map_chr
 #' @importFrom tidyr unite
+#' @importFrom Matrix colSums
 #'
 #' @docType methods
 #' @rdname keep_variable-methods
@@ -1716,7 +1717,7 @@ setMethod("keep_variable",
 			min.count = minimum_counts,
 			group = string_factor_of_interest,
 			min.prop = minimum_proportion,
-			lib.size = colSums(., na.rm=TRUE)
+			lib.size = Matrix::colSums(., na.rm=TRUE)
 		) %>%
 		not() %>%
 		which %>%