From e81ec84a169f6092c6002908cd7d11fa889b43fc Mon Sep 17 00:00:00 2001
From: LiNk-NY <marcel.ramos@roswellpark.org>
Date: Mon, 8 Jul 2024 12:42:40 -0400
Subject: [PATCH] bug fix: longFormat rowname type should be character, closes
 #331

---
 R/MultiAssayExperiment-helpers.R                  |  5 ++++-
 .../testthat/test-MultiAssayExperiment-helpers.R  | 15 +++++++++++++++
 2 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/R/MultiAssayExperiment-helpers.R b/R/MultiAssayExperiment-helpers.R
index be28e4d..a1a3493 100644
--- a/R/MultiAssayExperiment-helpers.R
+++ b/R/MultiAssayExperiment-helpers.R
@@ -351,9 +351,12 @@ setMethod("mergeReplicates", "ANY",
     if (!requireNamespace("reshape2", quietly = TRUE))
         stop("Package 'reshape2' is required for 'longFormat()' conversion")
 
-    reshape2::melt(
+    res <- reshape2::melt(
         object, varnames = c("rowname", "colname"), value.name = "value"
     )
+    if (!is.character(res[["rowname"]]))
+        res[["rowname"]] <- as.character(res[["rowname"]])
+    res
 }
 
 .longFormatElist <- function(object, i) {
diff --git a/tests/testthat/test-MultiAssayExperiment-helpers.R b/tests/testthat/test-MultiAssayExperiment-helpers.R
index a675440..6fc512f 100644
--- a/tests/testthat/test-MultiAssayExperiment-helpers.R
+++ b/tests/testthat/test-MultiAssayExperiment-helpers.R
@@ -254,4 +254,19 @@ test_that(".longFormatANY works", {
                 Reduce(union, rownames(miniACC))
         )
     )
+
+    m <- matrix(1:12, nrow = 4)
+    colnames(m) <- LETTERS[1:3]
+    se <- SummarizedExperiment(m)
+    rownames(se) <- c(1, 2, 4, 5)
+
+    mae <- MultiAssayExperiment(list(x = se))
+    longformat <- longFormat(mae)
+    expect_true(
+        is.character(longformat[["rowname"]])
+    )
+    expect_identical(
+        typeof(m),
+        typeof(longformat[["value"]])
+    )
 })