use Matrix library for sparse counts

stemangiola · Sep 8, 2023 · 14848e8 · 14848e8
1 parent 1b4cace
commit 14848e8
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Showing 2 changed files with 3 additions and 1 deletion.
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
@@ -1584,6 +1584,7 @@ setMethod("keep_variable",
 #'
 #' @importFrom purrr map_chr
 #' @importFrom tidyr unite
+#' @importFrom Matrix colSums
 #'
 #' @docType methods
 #' @rdname keep_variable-methods
@@ -1711,7 +1712,7 @@ 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 %>%