gdrplatform · bczech · Apr 16, 2026 · Apr 14, 2026 · Apr 14, 2026 · Apr 14, 2026
@@ -1,8 +1,8 @@
 Package: gDRutils
 Type: Package
 Title: A package with helper functions for processing drug response data
-Version: 1.9.6
-Date: 2026-03-23
+Version: 1.9.7
+Date: 2026-04-14
 Authors@R: c(person("Bartosz", "Czech", role=c("aut"),
                    comment = c(ORCID = "0000-0002-9908-3007")),
              person("Arkadiusz", "Gladki", role=c("cre", "aut"), email="gladki.arkadiusz@gmail.com",

@@ -1,3 +1,6 @@
+## gDRutils 1.9.7 - 2026-04-14
+* add support for metadata in `merge_MAE`
+
 ## gDRutils 1.9.6 - 2026-03-23
 * `standardize_MAE` standardizes also internal identifiers
 

@@ -6,12 +6,16 @@
 #' that can arise from multiple projects.
 #' @param discard_keys Character vector of strings that will be discarded
 #' during creating BumpyMatrix object.
+#' @param title String specifying the final DataSetDB title. If NULL, auto-generates.
+#' @param description String specifying the final DataSetDB description. If NULL, auto-generates.
+#' @param source_name String specifying the standard DSDB source name. If NULL, auto-detects or uses "merged_analysis".
+#' @param source_id String specifying the unique DSDB source ID. If NULL, uses "merged_dataset".
 #' @keywords SE_operators
 #'
 #' @examples
 #' mae1 <- get_synthetic_data("finalMAE_combo_2dose_nonoise")
 #' mae2 <- get_synthetic_data("finalMAE_combo_2dose_nonoise")
-#' merge_MAE(list(mae1 = mae1, mae2 = mae2))
+#' merge_MAE(list(mae1 = mae1, mae2 = mae2), title = "Test", description = "Test MAE")
 #'
 #' @return Merged MultiAssayExperiment object.
 #' @export
@@ -25,28 +29,112 @@ merge_MAE <- function(MAElist,
                                        "control_type",
                                        "iso_level",
                                        "conc_1",
-                                       "conc_2")) {
+                                       "conc_2"),
+                      title = NULL,
+                      description = NULL,
+                      source_name = NULL,
+                      source_id = NULL) {
 
   checkmate::assert_list(MAElist, types = "MultiAssayExperiment")
+  checkmate::assert_string(title, null.ok = TRUE)
+  checkmate::assert_string(description, null.ok = TRUE)
+  checkmate::assert_string(source_name, null.ok = TRUE)
+  checkmate::assert_string(source_id, null.ok = TRUE)
 
   experiments <- unique(unlist(lapply(MAElist, names)))
 
   merged_SE_assays <- lapply(experiments, function(exp_name) {
     exp_list <- lapply(MAElist, function(mae) {
-      if (exp_name %in% names(mae)) {
-        mae[[exp_name]]
-      } else {
-        NULL
-      }
+      if (exp_name %in% names(mae)) mae[[exp_name]] else NULL
     })
     exp_list <- exp_list[!vapply(exp_list, is.null, FUN.VALUE = logical(1))]
     merge_SE(exp_list)
   })
   names(merged_SE_assays) <- experiments
 
+  mae_names <- names(MAElist)
+  if (is.null(mae_names) || all(trimws(mae_names) == "")) {
+    mae_names <- paste0("Dataset_", seq_along(MAElist))
+  }
+
+  all_sources <- list()
+  original_titles <- c()
+
+  for (mae in MAElist) {
+    for (exp in names(mae)) {
+      meta <- as.list(S4Vectors::metadata(mae[[exp]])$experiment_metadata)
+      if (length(meta) > 0) {
+        if (is.list(meta$sources)) all_sources <- c(all_sources, meta$sources)
+        if (!is.null(meta$title)) original_titles <- c(original_titles, meta$title)
+      }
+    }
+  }
+
+
+  if (is.null(title)) {
+    title <- sprintf("Merged MAE: %s", paste(mae_names, collapse = " + "))
+  }
+
+  if (is.null(description)) {
+    description <- sprintf("Synthetically merged dataset originating from: %s.", paste(mae_names, collapse = ", "))
+    unique_titles <- unique(original_titles)
+    if (length(unique_titles) > 0) {
+      description <- paste0(description, " Original Titles: [", paste(unique_titles, collapse = " | "), "]")
+    }
+  }
+
+  if (is.null(source_name)) {
+    if (length(all_sources) > 0) {
+      unique_names <- unique(vapply(all_sources, function(s) {
+        if (!is.null(s$name)) s$name else "unknown"
+      }, character(1)))
+
+      source_name <- if (length(unique_names) == 1 && unique_names[1] != "unknown") {
+        unique_names[1]
+      } else {
+        "merged_analysis"
+      }
+    } else {
+      source_name <- "merged_analysis"
+    }
+  }
+
+  if (is.null(source_id)) {
+    source_id <- "merged_dataset"
+  }
+
+  synthetic_experiment_metadata <- list(
+    title = title,
+    description = description,
+    experimentalist = Sys.info()[["user"]],
+    sources = list(list(name = source_name, id = source_id))
+  )
+
+  for (i in seq_along(merged_SE_assays)) {
+    meta_list <- as.list(S4Vectors::metadata(merged_SE_assays[[i]]))
+    meta_list$experiment_metadata <- synthetic_experiment_metadata
+    S4Vectors::metadata(merged_SE_assays[[i]]) <- meta_list
+  }
+
+  base_metadata <- as.list(S4Vectors::metadata(MAElist[[1]]))
+  if (length(base_metadata) == 0) base_metadata <- list()
+
+  if (!is.null(base_metadata$.internal$DataSetDB$dataset)) {
+    ds_meta <- as.list(base_metadata$.internal$DataSetDB$dataset)
+    ds_meta$title <- synthetic_experiment_metadata$title
+    ds_meta$description <- synthetic_experiment_metadata$description
+    ds_meta$sources <- synthetic_experiment_metadata$sources
+
+    internal_meta <- as.list(base_metadata$.internal)
+    internal_meta$DataSetDB <- as.list(internal_meta$DataSetDB)
+    internal_meta$DataSetDB$dataset <- ds_meta
+
+    base_metadata$.internal <- internal_meta
+  }
+
   MultiAssayExperiment::MultiAssayExperiment(
     experiments = MultiAssayExperiment::ExperimentList(merged_SE_assays),
-    metadata = Reduce(c, lapply(MAElist, S4Vectors::metadata))
+    metadata = base_metadata
   )
 }
 
@@ -207,7 +295,6 @@ merge_assay <- function(SElist,
   list(DT = DT, BM = BM)
 }
 
-
 #' Identify unique metadata fields from a list of \code{SummarizedExperiment}s
 #'
 #' @param SElist named list of \code{SummarizedExperiment}s
@@ -233,7 +320,6 @@ identify_unique_se_metadata_fields <- function(SElist) {
   })))
 }
 
-
 #' Merge metadata
 #'
 #' @param SElist named list of \code{SummarizedExperiment}s
@@ -261,12 +347,52 @@ merge_metadata <- function(SElist,
   checkmate::assert_character(metadata_fields)
 
   all_metadata <- lapply(metadata_fields, function(x) {
+
+    if (x %in% c("experiment_metadata", ".internal")) {
+
+      valid_metas <- lapply(SElist, function(se) S4Vectors::metadata(se)[[x]])
+      valid_metas <- valid_metas[!vapply(valid_metas, is.null, FUN.VALUE = logical(1))]
+
+      if (length(valid_metas) == 0) return(list())
+
+      if (x == "experiment_metadata") {
+        synth <- as.list(valid_metas[[1]]) 
+
+        all_sources <- list()
+        for (vm in valid_metas) {
+          vm_list <- as.list(vm)
+          if (is.list(vm_list$sources)) all_sources <- c(all_sources, vm_list$sources)
+        }
+
+        if (length(all_sources) > 0) {
+          unique_names <- unique(vapply(all_sources, function(s) {
+            if (!is.null(s$name)) s$name else "unknown"
+          }, character(1)))
+
+          std_name <- if (length(unique_names) == 1 && unique_names[1] != "unknown") {
+            unique_names[1]
+          } else {
+            "merged_analysis"
+          }
+
+          synth$sources <- list(list(name = std_name, id = "merged_dataset"))
+        } else {
+          synth$sources <- list()
+        }
+
+        return(synth)
+      }
+
+      return(as.list(valid_metas[[1]]))
+    }
+
     do.call(c, lapply(names(SElist), function(SE) {
       meta <- list(S4Vectors::metadata(SElist[[SE]])[[x]])
       names(meta) <- SE
       meta
     }))
   })
+
   names(all_metadata) <- metadata_fields
   all_metadata
 }
@@ -5,7 +5,7 @@ listSE <- lapply(listMAE, function(x) x[[2]])
 names(listSE) <- c("combo1", "combo2")
 
 listMAE2 <- lapply(list.files(system.file(package = "gDRtestData", "testdata"),
-                             "final", full.names = TRUE)[1:2], qs::qread)
+                              "final", full.names = TRUE)[1:2], qs::qread)
 listSE2 <- lapply(listMAE, function(x) x[[1]])
 names(listSE2) <- c("combo1", "combo2")
 
@@ -28,8 +28,11 @@ test_that("merge_metadata and identify_unique_se_metadata_fields work as expecte
   metadata_fields <- identify_unique_se_metadata_fields(listSE)
   mergedMetadata <- merge_metadata(listSE, metadata_fields)
   expect_identical(names(mergedMetadata), metadata_fields)
-  expect_identical(names(mergedMetadata$experiment_metadata), names(listSE))
 
+  if ("experiment_metadata" %in% names(mergedMetadata)) {
+    expect_true("sources" %in% names(mergedMetadata$experiment_metadata))
+  }
+
   listSE2 <- listSE
   newMetaName <- "dummy_meta"
   S4Vectors::metadata(listSE2$combo1)[[newMetaName]] <- list()
@@ -45,29 +48,31 @@ test_that("merge_SE works as expected", {
   checkmate::expect_class(mergedSE$result, "SummarizedExperiment")
   S4Vectors::metadata(mergedSE$result)[["df_raw_data"]] <- list(NULL)
   validate_SE(mergedSE$result)
+
   additional_col_name <- "QCS"
   mergedSE2 <- purrr::quietly(merge_SE)(listSE, additional_col_name)
   assayNormalized <- convert_se_assay_to_dt(mergedSE2$result, "Metrics") 
   expect_true(additional_col_name %in% names(assayNormalized))
   expect_identical(unique(assayNormalized[[additional_col_name]]), names(listSE))
   expect_identical(SummarizedExperiment::assayNames(listSE[[1]]),
-                   SummarizedExperiment::assayNames(mergedSE[[1]]))
+                   SummarizedExperiment::assayNames(mergedSE$result))
   reset_env_identifiers()
-  })
+})
 
 
 test_that("merge_SE works as expected with combo matrix data", {
   mergedSE <- purrr::quietly(merge_SE)(listSE2)
   checkmate::expect_class(mergedSE$result, "SummarizedExperiment")
   S4Vectors::metadata(mergedSE$result)[["df_raw_data"]] <- list(NULL)
   validate_SE(mergedSE$result)
+
   additional_col_name <- "QCS"
   mergedSE2 <- purrr::quietly(merge_SE)(listSE2, additional_col_name)
   assayNormalized <- convert_se_assay_to_dt(mergedSE2$result, "Metrics") 
   expect_true(additional_col_name %in% names(assayNormalized))
   expect_identical(unique(assayNormalized[[additional_col_name]]), names(listSE))
   expect_identical(SummarizedExperiment::assayNames(listSE2[[1]]),
-                   SummarizedExperiment::assayNames(mergedSE[[1]]))
+                   SummarizedExperiment::assayNames(mergedSE$result))
 })
 
 test_that("merge_SE works as expected with mixed data types", {
@@ -85,10 +90,28 @@ test_that("merge_SE works with data with additional perturbations", {
   expect_equal(dim(mergedSE$result), c(10, 5))
 })
 
-test_that("merge_MAE works as expected", {
-  mergedMAE <- purrr::quietly(merge_MAE)(listMAE)
+test_that("merge_MAE works as expected with synthetic metadata injection", {
+  custom_title <- "Unit Test Merged MAE"
+  custom_source_id <- "test_dataset_001"
+
+  mergedMAE <- purrr::quietly(merge_MAE)(
+    listMAE, 
+    title = custom_title,
+    source_id = custom_source_id
+  )
   checkmate::expect_class(mergedMAE$result, "MultiAssayExperiment")
   validate_MAE(mergedMAE$result)
+
+  mae_meta <- S4Vectors::metadata(mergedMAE$result)
+  if (!is.null(mae_meta$.internal$DataSetDB$dataset)) {
+    expect_equal(mae_meta$.internal$DataSetDB$dataset$title, custom_title)
+    expect_equal(mae_meta$.internal$DataSetDB$dataset$sources[[1]]$id, custom_source_id)
+  }
+
+  se_meta <- S4Vectors::metadata(mergedMAE$result[[1]])$experiment_metadata
+  expect_equal(se_meta$title, custom_title)
+  expect_equal(se_meta$sources[[1]]$id, custom_source_id)
+
   expect_identical(
     SummarizedExperiment::assayNames(MultiAssayExperiment::experiments(listMAE[[1]])[[1]]),
     SummarizedExperiment::assayNames(MultiAssayExperiment::experiments(mergedMAE$result)[[1]])