Merge pull request #131 from gdrplatform/GDR-2526

Gdr 2526
gdrplatform · Sep 10, 2024 · d40cd77 · d40cd77
2 parents 23a1244 + bc56176
commit d40cd77
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Showing 3 changed files with 18 additions and 9 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: gDRutils
 Type: Package
 Title: A package with helper functions for processing drug response data
-Version: 1.3.11
-Date: 2024-08-30
+Version: 1.3.12
+Date: 2024-09-04
 Authors@R: c(person("Bartosz", "Czech", role=c("aut"),
                    comment = c(ORCID = "0000-0002-9908-3007")),
              person("Arkadiusz", "Gladki", role=c("cre", "aut"), email="[email protected]",

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,6 @@
+## gDRutils 1.3.12 - 2024-09-04
+* remove hack with checkDimnames
+
 ## gDRutils 1.3.11 - 2024-08-30
 * remove GDS fit_source from gDRviz
 

diff --git a/R/merge_SE.R b/R/merge_SE.R
@@ -65,24 +65,30 @@ merge_SE <- function(SElist,
 
   metadata <- merge_metadata(SElist, metadataNames)
   metadata <- c(metadata, identifiers)
+
+  assays <- lapply(
+    merged_assays,
+    FUN = function(x) {
+      bm_assay <- x[["BM"]]
+      colnames(bm_assay) <- rownames(data$condition_md)
+      rownames(bm_assay) <- rownames(data$treatment_md)
+      bm_assay
+    }
+  )
+
   p_list <-
     list(
-      assays = lapply(merged_assays, "[[", "BM"),
+      assays = assays,
       colData = data$condition_md,
       rowData = data$treatment_md,
-      metadata = metadata,
-      checkDimnames = FALSE
+      metadata = metadata
     )
   av_pnames <-
     names(formals(SummarizedExperiment::SummarizedExperiment))
   f_list <- p_list[intersect(names(p_list), av_pnames)]
   do.call(SummarizedExperiment, f_list)
 }
 
-# 2021.11.01 - param checkDimnames was added to Summarized Experiment in Bioc 3.14, 
-# to make it compatible with previous solution we re filtering it 'checkDimnames' if not present
-# TODO: remove once all our envs are with Bioc 3.14
-
 #' Merge assay data
 #'
 #' @param SElist named list of Summarized Experiments