Merge pull request #158 from gdrplatform/GDR-2646

chore: bump version and update NEWS.md
gdrplatform · Aug 8, 2024 · 9ffc15a · 9ffc15a
2 parents 20eb5e7 + 5b8a87c
commit 9ffc15a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,8 +2,8 @@ Type: Package
 Package: gDRcore
 Title: Processing functions and interface to process and analyze drug
     dose-response data
-Version: 1.3.7
-Date: 2024-08-05
+Version: 1.3.8
+Date: 2024-08-08
 Authors@R: c(
     person("Bartosz", "Czech", , "[email protected]", role = "aut",
            comment = c(ORCID = "0000-0002-9908-3007")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,6 @@
+## gDRcore 1.3.8 - 2024-08-08
+* fix issue with mapping overrides untreated controls
+
 ## gDRcore 1.3.7 - 2024-08-05
 * fix issue with non-avearaged concentration data
 

diff --git a/R/map_df.R b/R/map_df.R
@@ -123,7 +123,7 @@ map_df <- function(trt_md,
 
   out <- lapply(seq_along(trt_rnames), function(i) {
     treatment <- trt_rnames[i]
-    if (is.na(exact_out[[treatment]]) || !is.null(override_untrt_controls)) {
+    if (all(is.na(exact_out[[treatment]])) || !is.null(override_untrt_controls)) {
 
       refs <- lapply(present_ref_cols, function(y) {
         unname(unlist(ref_md[, y, with = FALSE]) == unlist(trt_md[which(trt_md$rn == treatment),
@@ -149,7 +149,7 @@ map_df <- function(trt_md,
       # are found.
       idx <- idx * match_mx[matchFactor, ]
 
-      if (any(idx > 0)) {
+      if (any(idx > 0, na.rm = TRUE)) {
         match_idx <- which.max(idx)
         msgs <- c(
           msgs, 

diff --git a/tests/testthat/test-map_df.R b/tests/testthat/test-map_df.R
@@ -23,16 +23,57 @@ test_that("map_df works as expected", {
 
   expect_equal(mapping, out)
   expect_equal(sort(unique(unname(unlist(mapping)))), sort(rownames(ref_df)))
+
+  # Test Day0 data with E2
+
+  trt_dt <- data.table::data.table(
+    clid = c("Cell123456", "Cell123456", "Cell654321", "Cell654321"),
+    CellLineName = c("CellLineA", "CellLineA", "CellLineB", "CellLineB"),
+    Tissue = c("Liver", "Liver", "Liver", "Liver"),
+    parental_identifier = c("ParentA", "ParentA", "ParentB", "ParentB"),
+    subtype = c("type1", "type1", "type2", "type2"),
+    ReferenceDivisionTime = c(45, 45, 30, 30),
+    Gnumber = c("Drug12345678", "Drug12345678", "Drug87654321", "Drug87654321"),
+    DrugName = c("DrugX", "DrugX", "DrugY", "DrugY"),
+    drug_moa = c("MOA1", "MOA1", "MOA2", "MOA2"),
+    Duration = c(120, 120, 120, 120),
+    E2 = c("0", "0.0023", "0", "0.0023"),
+    rn = c("1", "2", "6", "7")
+  )
+
+  ref_dt <- data.table::data.table(
+    clid = c("Cell123456", "Cell123456", "Cell123456", "Cell654321", "Cell654321", "Cell654321"),
+    CellLineName = c("CellLineA", "CellLineA", "CellLineA", "CellLineB", "CellLineB", "CellLineB"),
+    Tissue = c("Liver", "Liver", "Liver", "Liver", "Liver", "Liver"),
+    parental_identifier = c("ParentA", "ParentA", "ParentA", "ParentB", "ParentB", "ParentB"),
+    subtype = c("type1", "type1", "type1", "type2", "type2", "type2"),
+    ReferenceDivisionTime = c(NA, NA, NA, 60, 60, 60),
+    Gnumber = c("Drug12345678", "Drug12345678", "Drug12345678", "Drug87654321", "Drug87654321", "Drug87654321"),
+    DrugName = c("DrugX", "DrugX", "DrugX", "DrugY", "DrugY", "DrugY"),
+    drug_moa = c("MOA1", "MOA1", "MOA1", "MOA2", "MOA2", "MOA2"),
+    Duration = c(0, 168, 168, 0, 168, 168),
+    E2 = c("0", "0", "0.0023", "0", "0", "0.0023"),
+    rn = c("3", "4", "5", "8", "9", "10")
+  )
+
+  ref_cols <- c("CellLineName", "Tissue", "parental_identifier", "subtype", 
+                "Barcode", "clid")
+
+  ref_type <- "Day0"
+  map_override_untrt_controls <- map_df(trt_dt,
+                                        ref_dt,
+                                        ref_cols = ref_cols,
+                                        ref_type = ref_type,
+                                        override_untrt_controls = c(E2 = 0.0023))
+  expect_list(map_override_untrt_controls)
+  expect_length(map_override_untrt_controls, 4)
 })
 
 
-
 # TODO: test_that("Best match is detected for missing controls", {}) # nolint
 
-
 # TODO: test_that("NAs are returned for missing controls", {}) # nolint
 
-
 mat_elem <- data.table::data.table(DrugName = rep(c("untreated", "drugA", "drugB", "untreated"), 2),
                                    DrugName_2 = rep(c("untreated", "vehicle", "drugA", "drugB"), 2),
                                    clid = rep(c("C1", "C2"), each = 4))