Filter out duplicated gene names in each reference dataset.

This ensures that we don't grab the wrong gene when mapping from marker names
back to row indices for entry into the C++ code.

R/trainSingleR.R

@@ -199,6 +199,7 @@
 #' @importFrom beachmat initializeCpp
 #' @importFrom S4Vectors List
 #' @importFrom SummarizedExperiment assay
+#' @importFrom DelayedArray DelayedArray
 trainSingleR <- function(
     ref, 
     labels, 
@@ -248,11 +249,17 @@ trainSingleR <- function(
     for (l in seq_along(ref)) {
         curref <- .to_clean_matrix(ref[[l]], assay.type, check.missing, msg="ref", num.threads=num.threads)
 
+        # Removing duplicated names and missing labels.
+        if (anyDuplicated(rownames(curref))) {
+            keep <- !duplicated(rownames(curref))
+            curref <- DelayedArray(curref)[keep,,drop=FALSE]
+        }
+
         curlabels <- as.character(labels[[l]])
         stopifnot(length(curlabels) == ncol(curref))
         keep <- !is.na(curlabels)
         if (!all(keep)) {
-            curref <- curref[,keep,drop=FALSE]
+            curref <- DelayedArray(curref)[,keep,drop=FALSE]
             curlabels <- curlabels[keep]
         }
 

tests/testthat/test-train.R

@@ -240,5 +240,17 @@ test_that("trainSingleR auto-eliminates NA labels", {
     out <- trainSingleR(training, training$label)
     ref <- trainSingleR(training[,!populate], training$label[!populate])
     expect_identical(out$labels, ref$labels)
-    expect_identical(out$ref, ref$ref)
+    expect_identical(as.matrix(out$ref), ref$ref)
+})
+
+test_that("trainSingleR auto-eliminates duplicate row names", {
+    expect_identical(anyDuplicated(rownames(training)), 0L) # make sure there weren't any to begin with.
+
+    rownames(training) <- head(rep(rownames(training), each=2), nrow(training))
+    out <- trainSingleR(training, training$label)
+
+    keep <- !duplicated(rownames(training))
+    ref <- trainSingleR(training[keep,], training$label)
+    expect_identical(out$labels, ref$labels)
+    expect_identical(as.matrix(out$ref), ref$ref)
 })