fix combat_seq for SE

stemangiola · Jul 24, 2023 · c2545c0 · c2545c0
1 parent 7d0d68e
commit c2545c0
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/R/methods_SE.R b/R/methods_SE.R
@@ -872,7 +872,7 @@ setMethod("remove_redundancy",
 
 	    my_assay_adjusted =
 	      my_assay_adjusted |>
-	      sva::ComBat_seq(batch = my_batch[,i],
+	      sva::ComBat_seq(batch = my_batch[,i] |> pull(1),
 	                    covar_mod = design,
 	                    full_mod=TRUE,
 	                    ...)

diff --git a/tests/testthat/test-bulk_methods_SummarizedExperiment.R b/tests/testthat/test-bulk_methods_SummarizedExperiment.R
@@ -203,8 +203,8 @@ test_that("Get adjusted counts multiple factors - SummarizedExperiment",{
 
   res =
     cm |>
-    adjust_abundance(.factor_unwanted = c(time, batch),
-                     .factor_of_interest = dead,
+    adjust_abundance(.factor_unwanted = c(batch),
+                     .factor_of_interest = time,
                      .abundance = count_scaled,
       method = "combat_seq",
       shrink.disp = TRUE,