add tests

mschemmel · Jun 30, 2024 · bd5105c · bd5105c
1 parent 2417b07
commit bd5105c
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Showing 6 changed files with 60 additions and 10 deletions.
diff --git a/man/assert.Rd b/man/assert.Rd
diff --git a/man/detect_reference.Rd b/man/detect_reference.Rd
diff --git a/man/in_range.Rd b/man/in_range.Rd
diff --git a/man/prepare.Rd b/man/prepare.Rd
diff --git a/tests/testthat/test_backend.R b/tests/testthat/test_backend.R
@@ -29,3 +29,14 @@ test_that("prepare() works", {
     df$efficiency <- 40
     expect_equal(unique(prepare(df)$E), 1.4)
 })
+
+test_that("conflate works()", {
+    run <- get_reference_group(qpcR(dat, hkg = "HKG", reference = "control", groups = "dpi", aggregate = FALSE))
+    control_groups <- aggregate(rexpr ~ gene + dpi, data = run, FUN = mean)
+    expect_equal(unique(control_groups$rexpr), c(1, 1))
+
+    run2 <- get_reference_group(qpcR(dat, hkg = c("HKG", "HKG2"), reference = "control", groups = "dpi", aggregate = FALSE))
+    control_groups2 <- aggregate(rexpr ~ gene + dpi, data = run2, FUN = mean)
+    expect_equal(unique(control_groups2$rexpr), c(1, 1))
+
+})
diff --git a/tests/testthat/test_qpcr.R b/tests/testthat/test_qpcr.R
@@ -1,14 +1,6 @@
 dat <- read.table("example2.tsv", sep = "\t", head = TRUE)
 
 test_that("qpcR() works", {
-    run <- get_reference_group(qpcR(dat, hkg = "HKG", reference = "control", groups = "dpi", aggregate = FALSE))
-    control_groups <- aggregate(rexpr ~ gene + dpi, data = run, FUN = mean)
-    expect_equal(unique(control_groups$rexpr), c(1, 1))
-
-    run2 <- get_reference_group(qpcR(dat, hkg = c("HKG", "HKG2"), reference = "control", groups = "dpi", aggregate = FALSE))
-    control_groups2 <- aggregate(rexpr ~ gene + dpi, data = run2, FUN = mean)
-    expect_equal(unique(control_groups2$rexpr), c(1, 1))
-
     expect_no_error(qpcR(dat, hkg = "HKG", groups = "dpi", outlier.method = "interquartile"))
     expect_no_error(qpcR(dat, hkg = "HKG", groups = "dpi", outlier.method = "z-score"))
     expect_no_error(qpcR(dat, hkg = "HKG", groups = "dpi", outlier.method = "hampel"))
@@ -18,6 +10,11 @@ test_that("qpcR() works", {
     expect_no_error(qpcR(dat, hkg = c("HKG", "HKG2"), groups = "dpi", outlier.method = "hampel"))
 })
 
+test_that("expression values of reference group equals 1", {
+    res <- qpcR(dat, hkg = "HKG", reference = "control", groups = "dpi", aggregate = TRUE)
+    expect_equal(unique(res[res == "control", ]$rexpr.mean, ), c(1, 1))
+})
+
 test_that("output equals data.frame", {
     expect_type(qpcR(dat, hkg = "HKG", groups = "dpi"), "list")
     expect_type(qpcR(dat, hkg = c("HKG", "HKG2"), groups = "dpi"), "list")