Merge pull request #32 from timoast/sparse_warning

Avoid warning when creating assay from non-dgCMatrix
satijalab · Nov 23, 2021 · fd32116 · fd32116
2 parents 5499191 + 6b6f48f
commit fd32116
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Showing 3 changed files with 8 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: SeuratObject
 Type: Package
 Title: Data Structures for Single Cell Data
-Version: 4.0.3.9001
-Date: 2021-11-19
+Version: 4.0.3.9002
+Date: 2021-11-23
 Authors@R: c(
   person(given = 'Rahul', family = 'Satija', email = 'rsatija@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0001-9448-8833')),
   person(given = 'Andrew', family = 'Butler', email = 'abutler@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0003-3608-0463')),

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,7 @@
 # Unreleased
 ## Changed
 - `CreateSeuratObject.Assay` sets Assay key when not present (#29)
+- Ignore warnings when creating an `Assay` from a data frame (#32)
 
 ## Added
 - New `CheckMatrix` generic for validating expression matrices

diff --git a/R/assay.R b/R/assay.R
@@ -129,7 +129,11 @@ CreateAssayObject <- function(
       stop("No feature names (rownames) names present in the input matrix")
     }
     if (!inherits(x = counts, what = 'dgCMatrix')) {
-      counts <- as.sparse(x = counts, ...)
+      if (inherits(x = counts, what = "data.frame")) {
+        counts <- as.sparse(x = counts, ...)
+      } else {
+        counts <- as.sparse(x = counts)
+      }
     }
     if (isTRUE(x = check.matrix)) {
       CheckMatrix(object = counts)