Fixing tests

BioinformaticsFMRP · May 22, 2023 · 3b51a98 · 3b51a98
1 parent b6b7e5a
commit 3b51a98
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/R/prepare.R b/R/prepare.R
@@ -139,7 +139,7 @@ GDCprepare <- function(
     }
 
     cases <- ifelse(
-        grepl("TCGA|TARGET|CGCI-HTMCP-CC|CPTAC-3",query$results[[1]]$project %>% unlist()),
+        grepl("TCGA|TARGET|CGCI-HTMCP-CC",query$results[[1]]$project %>% unlist()),
         query$results[[1]]$cases,
         query$results[[1]]$sample.submitter_id
     )

diff --git a/tests/testthat/test-prepare-download.R b/tests/testthat/test-prepare-download.R
@@ -156,7 +156,7 @@ test_that("Gene Level Copy Number is being correctly prepare", {
     data <- GDCprepare(query,directory = "ex")
 
     expect_true(all(substr(colnames(data),1,12) == c("TCGA-OR-A5JD","TCGA-OR-A5J7")))
-    expect_true(data$days_to_last_follow_up == c(3038,NA))
+    expect_equal(data$days_to_last_follow_up,c(3038,NA))
     unlink("ex", recursive = TRUE, force = TRUE)
 })
 
@@ -174,8 +174,8 @@ test_that("Gene Level Copy Number is being correctly prepare for CPTAC-3", {
     GDCdownload(query_CPTAC,directory = "ex")
     data <- GDCprepare(query_CPTAC,directory = "ex")
     expect_true(ncol(data) == 2)
-    expect_true(data$submitter_id == c("C3L-02544","C3N-01179"))
-    expect_true(data$days_to_last_follow_up == c("889","1816"))
+    expect_equal(data$submitter_id, c("C3L-02544","C3N-01179"))
+    expect_equal(data$days_to_last_follow_up, c("889","1816"))
     unlink("ex", recursive = TRUE, force = TRUE)
 })