satijalab · satijalab · Sep 7, 2020 · Jul 17, 2020 · Jul 17, 2020 · Jul 17, 2020
diff --git a/NEWS.md b/NEWS.md
@@ -17,6 +17,8 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 - Fix logging bug when functions were run via `do.call()`
 - Fix handling of weight.by.var parameter when approx=FALSE in `RunPCA()`
 
+### Deprecated
+- `CreateActivityMatrix` deprecated in favor of `Signac::GeneActivity`
 
 ## [3.2.0] - 2020-07-15
 ### Added

diff --git a/R/preprocessing.R b/R/preprocessing.R
@@ -184,6 +184,15 @@ CreateGeneActivityMatrix <- function(
   keep.sparse = FALSE,
   verbose = TRUE
 ) {
+  .Deprecated(
+    new = 'Signac::GeneActivity',
+    msg = paste(
+      "CreateGeneActivityMatrix functionality is being moved to Signac.",
+      "Equivalent functionality can be",
+      "achieved via the Signac::GeneActivity function; for",
+      "more information on Signac, please see https://github.com/timoast/Signac"
+    )
+  )
   if (!PackageCheck('GenomicRanges', error = FALSE)) {
     stop("Please install GenomicRanges from Bioconductor.")
   }