calcInteger knnSmooth warning

Author: darlanminussi

R/calcInteger.R

@@ -59,6 +59,14 @@ calcInteger <- function(scCNA,
   # args
   assay = match.arg(assay)
 
+
+  if (!is.null(assay(scCNA, 'smoothed_bincounts'))) {
+    warning("CopyKit detected that knnSmooth() has been performed.
+If working with knnSmooth datasets we recommend using assay segment_ratios:
+calcInteger(copykit, assay = 'segment_ratios')")
+  }
+
+  # getting datasets
   if (assay == 'bincounts') {
     bin <- SummarizedExperiment::assay(scCNA, 'bincounts')
   }