add unit test for function CreatePathwayCollection per issue #70

DESCRIPTION

@@ -35,7 +35,8 @@ Suggests:
     rmarkdown,
     SummarizedExperiment,
     survminer,
-    tidyverse
+    tidyverse,
+    testthat
 biocViews:
     CopyNumberVariation,
     DNAMethylation,

tests/testthat.R

@@ -0,0 +1,4 @@
+library(testthat)
+library(pathwayPCA)
+
+test_check("pathwayPCA")

tests/testthat/test_CreatePathwayCollection.R

@@ -0,0 +1,44 @@
+context("CreatePathwayCollection")
+
+test_that("CreatePathwayCollection gives correct errors", {
+  expect_error(CreatePathwayCollection(
+    sets_ls = "pathway",
+    TERMS = "five", 
+    setType = "pathway", 
+    setsize = 1
+  ), 
+  "The sets_ls object must be a list of set membership vectors.")
+
+  expect_error(CreatePathwayCollection(
+    sets_ls = list(one = 1, five = 5),
+    TERMS = list(five = "five"), 
+    setType = "pathway", 
+    setsize = 1
+  ), 
+  "The TERMS object must be an atomic vector.")
+
+  expect_error(CreatePathwayCollection(
+    sets_ls = list(one = 1, five = 5),
+    TERMS = "five", 
+    setType = "gene", 
+    setsize = 1
+  ), 
+  "The TERMS vector must have the same length as the sets list.")
+})
+
+test_that("CreatePathwayCollection gives correct warnings", {
+  expect_warning(CreatePathwayCollection(
+    sets_ls = list(one = 1,
+                   two = 1:2,
+                   three = 1:3,
+                   four = 1:4,
+                   five = 1:5),
+    TERMS = c("one", "two", "three", "four", "five"),
+    setType = "gene",
+    setsize = 1
+    ),
+    "The names 'setsize' and 'n_tested' are reserved names of a pathwayCollection object.
+            Values stored with these names may be overwritten during pathwayPCA function execution.
+            Use with extreme caution.")
+
+})