Fix tests and renaming runMetFamily() messed up by bad git merge

ipb-halle · Feb 27, 2024 · 5348757 · 5348757
1 parent 5a7defb
commit 5348757
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Showing 4 changed files with 14 additions and 71 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -44,7 +44,7 @@ biocViews: Software, Visualization
 Collate:
     'Annotation.R'
     'Classifiers.R'
-    'StartApp.R'
+    'runMetFamily.R'
     'R_packages.R'
     'FragmentMatrixFunctions.R'
     'DataProcessing.R'

diff --git a/man/parsePeakAbundanceMatrix.Rd b/man/parsePeakAbundanceMatrix.Rd
diff --git a/man/runMetFamily.Rd b/man/runMetFamily.Rd
diff --git a/tests/testthat/test_fileinput.R b/tests/testthat/test_fileinput.R
@@ -3,15 +3,19 @@ test_that("trivial", {
 })
 
 test_that("exampledata", {
-#   filePeakMatrix <- system.file("data/showcase/Metabolite_profile_showcase.txt", package = "MetFamily")
-#     data <- parsePeakAbundanceMatrix(filePeakMatrix, doPrecursorDeisotoping, 
-# 	mzDeviationInPPM_precursorDeisotoping, mzDeviationAbsolute_precursorDeisotoping, 
-# 	maximumRtDifference, 
-# 	progress=FALSE)
-# 
-#     expect_equal(nrow(data), 17)
-#     expect_equal(ncol(data), 34)
-# 
+  filePeakMatrix <- system.file("data/showcase/Metabolite_profile_showcase.txt", package = "MetFamily")
+  data <- parsePeakAbundanceMatrix(filePeakMatrix, doPrecursorDeisotoping=TRUE,
+                                   mzDeviationInPPM_precursorDeisotoping=10, mzDeviationAbsolute_precursorDeisotoping=0.01,
+                                   maximumRtDifference=0.05,
+                                   progress=FALSE)
+
+  ## Test dimensions  
+  expect_equal(nrow(data$dataFrame1), 5403)
+  expect_equal(ncol(data$dataFrame1),   20)
+
+  ## Test some values
+  expect_true(all(summary(t(data$dataFrame1[1,c("TRI03", "TRI02", "TRI01", "LVS03", "LVS02", "LVS01")])) == c("Min.   : 236.0  ", "1st Qu.: 306.2  ", "Median : 357.5  ", "Mean   : 501.0  ", "3rd Qu.: 554.2  ", "Max.   :1146.0  ")))
+  expect_true(all(round(summary(data$dataFrame1[, "TRI01"])) == c(0,     809,    1537,    9818,    3207, 4407926)))
 })
 
 test_that("MS-Dial 4.X", {