test: simplify create_deseq_obj check for counts matrix

CCBR · Dec 28, 2023 · 89875ab · 89875ab
1 parent f75c49f
commit 89875ab
Showing 1 changed file with 9 additions and 54 deletions.
diff --git a/tests/testthat/test-deseq2.R b/tests/testthat/test-deseq2.R
@@ -28,66 +28,21 @@ test_that("create_deseq_obj works", {
       )
     )
   )
-
-  # run deseq
-  dds_dex <- DESeq2::DESeq(dds, fitType = "local")
-  res <- DESeq2::results(dds_dex)
-  res_dat <- res %>% as.data.frame()
-  expect_true(all.equal(
-    res_dat %>% dplyr::filter(baseMean > 30),
+  expect_equal(
+    dds@assays@data@listData %>% as.data.frame() %>% dplyr::filter(counts.KO_S3 > 15),
     structure(
       list(
-        baseMean = c(
-          46.2022644566773,
-          33.9841778188053,
-          31.0208397331822,
-          30.6175122400626,
-          35.6755294108162
-        ),
-        log2FoldChange = c(
-          -0.93461130443384,
-          -3.35053555731274,
-          -4.88594876484931,
-          -4.43532926024883,
-          -1.8328208411504
-        ),
-        lfcSE = c(
-          0.267983882511375,
-          0.52224772094996,
-          0.860982558001587,
-          0.753983075954482,
-          0.36162525207182
-        ),
-        stat = c(
-          -3.48756535533128,
-          -6.41560589526015,
-          -5.67485220164042,
-          -5.88253158684504,
-          -5.0682877665479
-        ),
-        pvalue = c(
-          0.000487439776013235,
-          1.40263874605495e-10,
-          1.38808448089501e-08,
-          4.04038197166405e-09,
-          4.01410224129028e-07
-        ),
-        padj = c(
-          0.00389951820810588,
-          1.79537759495034e-08,
-          5.92249378515205e-07,
-          2.58584446186499e-07,
-          8.56341811475261e-06
-        )
+        counts.KO_S3 = c(25L, 16L, 19L),
+        counts.KO_S4 = c(22L, 10L, 26L),
+        counts.WT_S1 = c(74L, 0L, 10L),
+        counts.WT_S2 = c(104L, 0L, 8L)
       ),
       class = "data.frame",
       row.names = c(
         "ENSG00000185658.13",
-        "ENSG00000142156.14",
-        "ENSG00000142173.15",
-        "ENSG00000159140.20",
-        "ENSG00000182670.13"
+        "ENSG00000233922.2",
+        "ENSG00000157601.14"
       )
     )
-  ))
+  )
 })