Specific package to peakcombiner when loading data in tests

Novartis · Jan 29, 2025 · b463f2c · b463f2c
1 parent 4f3e11a
commit b463f2c
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Showing 14 changed files with 18 additions and 18 deletions.
diff --git a/tests/testthat/test-center_expand_regions.R b/tests/testthat/test-center_expand_regions.R
@@ -22,7 +22,7 @@ output_colnames_post <- c(
   "center", "sample_name", "input_names"
 )
 ##
-data(syn_data_bed)
+data(syn_data_bed, package = "peakCombiner")
 test_data <- syn_data_bed
 ##
 test_data_prepared <- peakCombiner::prepare_input_regions(
@@ -217,13 +217,13 @@ test_that("Output data frame is correct for post-combined", {
 test_that("Output data frame is correct for data_prepared", {
   ##
   data <- test_data_prepared
-  result <- center_expand_regions(
+  result <- peakCombiner::center_expand_regions(
     data = data,
     center_by = "center_column",
     expand_by = NULL
   )
   ##
-  expect_no_error(center_expand_regions(
+  expect_no_error(peakCombiner::center_expand_regions(
     data = data,
     center_by = "center_column",
     expand_by = NULL

diff --git a/tests/testthat/test-combine_regions.R b/tests/testthat/test-combine_regions.R
@@ -16,7 +16,7 @@ output_colnames <- c(
 )
 
 #' Prepare test data set
-data(syn_data_tibble)
+data(syn_data_tibble, package = "peakCombiner")
 test_data <- syn_data_tibble
 test_data
 

diff --git a/tests/testthat/test-cr_add_summit.R b/tests/testthat/test-cr_add_summit.R
@@ -18,7 +18,7 @@ output_colnames <- c(
   "sample_name", "input_names"
 )
 ##
-data(syn_data_tibble)
+data(syn_data_tibble, package = "peakCombiner")
 test_data <- syn_data_tibble
 ##
 test_data_prepared <- peakCombiner::prepare_input_regions(

diff --git a/tests/testthat/test-cr_disjoin_filter.R b/tests/testthat/test-cr_disjoin_filter.R
@@ -9,7 +9,7 @@ required_colnames <- c(
   "chrom", "start", "end", "name", "score", "strand", "center", "sample_name"
 )
 ##
-data(syn_data_tibble)
+data(syn_data_tibble, package = "peakCombiner")
 test_data <- syn_data_tibble
 input_colnames <- colnames(test_data)
 ##

diff --git a/tests/testthat/test-cr_overlap_with_summits.R b/tests/testthat/test-cr_overlap_with_summits.R
@@ -17,7 +17,7 @@ output_colnames <- c(
   "chrom", "start", "end", "width", "strand", "input_names"
 )
 ##
-data(syn_data_tibble)
+data(syn_data_tibble, package = "peakCombiner")
 test_data <- syn_data_tibble
 input_colnames <- colnames(test_data)
 ##

diff --git a/tests/testthat/test-cr_reduce.R b/tests/testthat/test-cr_reduce.R
@@ -12,7 +12,7 @@ input_colnames <- c(
 ##
 output_colnames <- c("chr", "start", "end", "width", "strand", "input_names")
 ##
-data(syn_data_tibble)
+data(syn_data_tibble, package = "peakCombiner")
 test_data <- syn_data_tibble
 ##
 test_data_prepared <- peakCombiner::prepare_input_regions(

diff --git a/tests/testthat/test-define_expansion.R b/tests/testthat/test-define_expansion.R
@@ -12,7 +12,7 @@ required_colnames <- c(
 ##
 test_expansion_value <- 350
 ##
-data(syn_data_tibble)
+data(syn_data_tibble, package = "peakCombiner")
 test_data <- syn_data_tibble
 input_colnames <- colnames(test_data)
 ##

diff --git a/tests/testthat/test-filter_by_blacklist.R b/tests/testthat/test-filter_by_blacklist.R
@@ -10,7 +10,7 @@ required_colnames <- c(
   "center", "sample_name"
 )
 ##
-data(syn_data_tibble)
+data(syn_data_tibble, package = "peakCombiner")
 test_data <- syn_data_tibble
 input_colnames <- colnames(test_data)
 ##
@@ -31,7 +31,7 @@ test_data_filtered <- peakCombiner:::filter_by_chromosome_names(
 ##
 input_colnames <- colnames(test_data_filtered)
 ##
-data(blacklist_hg38)
+data(blacklist_hg38, package = "peakCombiner")
 blacklist <- blacklist_hg38
 ##
 test_data_filtered_bl <- peakCombiner:::filter_by_blacklist(

diff --git a/tests/testthat/test-filter_by_chromosome_names.R b/tests/testthat/test-filter_by_chromosome_names.R
@@ -10,7 +10,7 @@ required_colnames <- c(
   "center", "sample_name"
 )
 ##
-data(syn_data_tibble)
+data(syn_data_tibble, package = "peakCombiner")
 test_data <- syn_data_tibble
 input_colnames <- colnames(test_data)
 ##

diff --git a/tests/testthat/test-filter_by_significance.R b/tests/testthat/test-filter_by_significance.R
@@ -10,7 +10,7 @@ required_colnames <- c(
   "center", "sample_name"
 )
 ##
-data(syn_data_tibble)
+data(syn_data_tibble, package = "peakCombiner")
 test_data <- syn_data_tibble
 input_colnames <- colnames(test_data)
 ##

diff --git a/tests/testthat/test-filter_by_top_enriched.R b/tests/testthat/test-filter_by_top_enriched.R
@@ -10,7 +10,7 @@ required_colnames <- c(
   "center", "sample_name"
 )
 ##
-data(syn_data_tibble)
+data(syn_data_tibble, package = "peakCombiner")
 test_data <- syn_data_tibble
 input_colnames <- colnames(test_data)
 ##

diff --git a/tests/testthat/test-filter_regions.R b/tests/testthat/test-filter_regions.R
@@ -10,7 +10,7 @@ required_colnames <- c(
   "center", "sample_name"
 )
 ##
-data(syn_data_tibble)
+data(syn_data_tibble, package = "peakCombiner")
 test_data <- syn_data_tibble
 
 input_colnames <- colnames(test_data)

diff --git a/tests/testthat/test-load_input_regions.R b/tests/testthat/test-load_input_regions.R
@@ -5,7 +5,7 @@
 ##
 set.seed(1234)
 ##
-data(syn_data_tibble)
+data(syn_data_tibble, package = "peakCombiner")
 test_data <- syn_data_tibble
 ##
 all_colnames <- c(

diff --git a/tests/testthat/test-prepare_input_regions.R b/tests/testthat/test-prepare_input_regions.R
@@ -12,14 +12,14 @@ colnames_preloaded_df <- c(
 
 allowed_file_format <- c("narrowpeak", "broadpeak", "bed")
 
-data(syn_data_bed)
+data(syn_data_bed, package = "peakCombiner")
 samplesheet_test <- syn_data_bed
 
 test_sample_sheet <- peakCombiner::prepare_input_regions(
   data = samplesheet_test[1, ]
 )
 
-data(syn_data_tibble)
+data(syn_data_tibble, package = "peakCombiner")
 test_data <- syn_data_tibble
 input_colnames <- colnames(test_data)