feat: emit merged DEG table for OMIX compatibility

.codeocean/app-panel.json

@@ -167,6 +167,9 @@
 	"results": [
 		{
 			"file_name": "figures/diff/mean-variance.png"
+		},
+		{
+			"file_name": "deg/DEG_Analysis.csv"
 		}
 	]
 }

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## Development version
 
+- Emit a merged, contrast-prefixed DEG table (`deg/DEG_Analysis.csv`) alongside the existing MOO output, for compatibility with downstream tools such as OMIX-GSEA-Preranked-Legacy that expect a flat DEG table (#9, @TJoshMeyer).
 - Sync Code Ocean app panel parameter descriptions with MOSuite package documentation for MOSuite v0.4.1 (#7, @phoman14).
 - Improved the Code Ocean parameter UI for the diff counts capsule (#3, @phoman14).
 - Use MOSuite v0.3.2. (#4, @kelly-sovacool)

code/main.R

@@ -88,7 +88,7 @@ if (identical(args$contrasts, "")) {
 }
 
 # run MOSuite
-moo |>
+moo_diff <- moo |>
   diff_counts(
     count_type = args$count_type,
     sub_count_type = args$sub_count_type,
@@ -104,5 +104,15 @@ moo |>
     input_in_log_counts = args$input_in_log_counts,
     return_mean_and_sd = args$return_mean_and_sd,
     voom_normalization_method = args$voom_normalization_method
-  ) |>
+  )
+
+moo_diff |>
   write_rds(file.path(getOption("moo_plots_dir"), "..", "moo", "moo-diff.rds"))
+
+# emit a merged, contrast-prefixed DEG table for downstream tools (e.g. OMIX)
+# that consume a flat table rather than a multiOmicDataSet
+deg_dir <- file.path(getOption("moo_plots_dir"), "..", "deg")
+dir.create(deg_dir, recursive = TRUE, showWarnings = FALSE)
+moo_diff@analyses$diff |>
+  join_dfs_wide() |>
+  write_csv(file.path(deg_dir, "DEG_Analysis.csv"))

tests/testthat/helper-cli.R

@@ -9,6 +9,7 @@ setup_cli_workspace <- function(prefix = "mosuite_diff_counts_test_") {
   dir.create(data_dir, recursive = TRUE)
   dir.create(file.path(results_dir, "figures"), recursive = TRUE)
   dir.create(file.path(results_dir, "moo"), recursive = TRUE)
+  dir.create(file.path(results_dir, "deg"), recursive = TRUE)
 
   repo_root <- normalizePath(
     file.path(testthat::test_path(), "..", ".."),
@@ -69,6 +70,22 @@ expect_outputs_created <- function(results_dir) {
     "diff" %in% names(moo@analyses),
     info = "Output should have diff results in moo@analyses"
   )
+
+  deg_path <- file.path(results_dir, "deg", "DEG_Analysis.csv")
+  expect_true(
+    file.exists(deg_path),
+    info = "Merged DEG table should be created"
+  )
+  expect_true(
+    file.info(deg_path)$size > 0,
+    info = "Merged DEG table should be non-empty"
+  )
+
+  deg_dat <- readr::read_csv(deg_path, show_col_types = FALSE)
+  expect_true(
+    all(c("B-A_logFC", "B-A_pval", "B-A_adjpval") %in% colnames(deg_dat)),
+    info = "Merged DEG table should have contrast-prefixed columns for OMIX compatibility"
+  )
 }
 
 common_cli_args <- c(