From 6d854207609c154603b348a3c564168f02c487c4 Mon Sep 17 00:00:00 2001 From: "Muckenhuber, Markus" Date: Wed, 29 Jan 2025 15:54:04 +0100 Subject: [PATCH] Add libary & refer to all functions with peakCombiner --- tests/testthat/test-center_expand_regions.R | 44 ++++++------- tests/testthat/test-combine_regions.R | 66 ++++++++++--------- tests/testthat/test-cr_add_summit.R | 36 +++++----- tests/testthat/test-cr_disjoin_filter.R | 24 ++++--- tests/testthat/test-cr_overlap_with_summits.R | 16 +++-- tests/testthat/test-cr_reduce.R | 12 ++-- tests/testthat/test-define_expansion.R | 6 +- tests/testthat/test-filter_by_blacklist.R | 36 +++++----- .../test-filter_by_chromosome_names.R | 18 ++--- tests/testthat/test-filter_by_significance.R | 20 +++--- tests/testthat/test-filter_by_top_enriched.R | 22 ++++--- tests/testthat/test-filter_regions.R | 23 +++---- tests/testthat/test-load_input_regions.R | 14 ++-- tests/testthat/test-prepare_input_regions.R | 10 +-- 14 files changed, 189 insertions(+), 158 deletions(-) diff --git a/tests/testthat/test-center_expand_regions.R b/tests/testthat/test-center_expand_regions.R index fb08ca0..2839c3d 100644 --- a/tests/testthat/test-center_expand_regions.R +++ b/tests/testthat/test-center_expand_regions.R @@ -23,18 +23,18 @@ output_colnames_post <- c( data(syn_data_bed) test_data <- syn_data_bed ## -test_data_prepared <- prepare_input_regions( +test_data_prepared <- peakCombiner::prepare_input_regions( data = test_data ) ## -test_data_center_expand <- center_expand_regions( +test_data_center_expand <- peakCombiner::center_expand_regions( data = test_data_prepared, center_by = "center_column", expand_by = NULL ) restult_colnames <- colnames(test_data_center_expand) ## -test_data_filtered <- filter_regions( +test_data_filtered <- peakCombiner::filter_regions( data = test_data_center_expand, exclude_by_blacklist = "hg38", # "hg38", include_by_chromosome_name = NULL, @@ -43,7 +43,7 @@ test_data_filtered <- filter_regions( show_messages = TRUE ) ## -test_data_combined <- combine_regions( +test_data_combined <- peakCombiner::combine_regions( data = test_data_filtered, found_in_samples = 2, combined_center = "nearest", @@ -51,7 +51,7 @@ test_data_combined <- combine_regions( combined_sample_name = "combined" ) ## -test_data_combined_ce <- center_expand_regions( +test_data_combined_ce <- peakCombiner::center_expand_regions( data = test_data_combined, center_by = "center_column", expand_by = NULL @@ -61,7 +61,7 @@ test_data_combined_ce <- center_expand_regions( ### -----------------------------------------------------------------------### testthat::test_that("Test if function works with pre-combined input", { - testthat::expect_no_error(center_expand_regions( + testthat::expect_no_error(peakCombiner::center_expand_regions( data = test_data_prepared, center_by = "center_column", expand_by = NULL @@ -69,7 +69,7 @@ testthat::test_that("Test if function works with pre-combined input", { }) testthat::test_that("Test if function works with post-combined input", { - testthat::expect_no_error(center_expand_regions( + testthat::expect_no_error(peakCombiner::center_expand_regions( data = test_data_combined, center_by = "center_column", expand_by = NULL @@ -112,27 +112,27 @@ test_that("Required input data has the expected structure", { ### -----------------------------------------------------------------------### test_that("Required paramter 'center_by' has the expected structure/value", { - expect_no_error(center_expand_regions( + expect_no_error(peakCombiner::center_expand_regions( data = test_data_prepared, center_by = "center_Column", expand_by = NULL )) - expect_error(center_expand_regions( + expect_error(peakCombiner::center_expand_regions( data = test_data_prepared, center_by = c("center_column", "calculated_value"), expand_by = NULL ), "center_by") - expect_error(center_expand_regions( + expect_error(peakCombiner::center_expand_regions( data = test_data_prepared, center_by = "nonexisting", expand_by = NULL ), "center_by") - expect_error(center_expand_regions( + expect_error(peakCombiner::center_expand_regions( data = test_data_prepared, center_by = NULL, expand_by = NULL ), "center_by") - expect_error(center_expand_regions( + expect_error(peakCombiner::center_expand_regions( data = test_data_prepared, center_by = NA, expand_by = NULL @@ -142,22 +142,22 @@ test_that("Required paramter 'center_by' has the expected structure/value", { ### -----------------------------------------------------------------------### testthat::test_that("Required paramter expand_by has the expected structure/value", { - testthat::expect_no_error(center_expand_regions( + testthat::expect_no_error(peakCombiner::center_expand_regions( data = test_data_prepared, center_by = "center_column", expand_by = NULL )) - testthat::expect_error(center_expand_regions( + testthat::expect_error(peakCombiner::center_expand_regions( data = test_data_prepared, center_by = "column_value", expand_by = NA ), ) - testthat::expect_error(center_expand_regions( + testthat::expect_error(peakCombiner::center_expand_regions( data = test_data_prepared, center_by = "column_value", expand_by = c(1, 2, 3) ), ) - testthat::expect_error(center_expand_regions( + testthat::expect_error(peakCombiner::center_expand_regions( data = test_data_prepared, center_by = "column_value", expand_by = "nonexisting" @@ -233,13 +233,13 @@ test_that("Output data frame is correct for data_prepared", { test_that("Output data frame is correct for data_center_expand", { ## data <- test_data_center_expand - 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 @@ -251,13 +251,13 @@ test_that("Output data frame is correct for data_center_expand", { test_that("Output data frame is correct for data_filtered", { ## data <- test_data_filtered - 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 @@ -269,13 +269,13 @@ test_that("Output data frame is correct for data_filtered", { test_that("Output data frame is correct for data_combined", { ## data <- test_data_combined - 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 index 0765a15..d3afd5e 100644 --- a/tests/testthat/test-combine_regions.R +++ b/tests/testthat/test-combine_regions.R @@ -3,6 +3,8 @@ ### Prepare data for testing ### -----------------------------------------------------------------------### ## +library(peakCombiner) +## set.seed(1234) ## input_colnames <- c( @@ -20,19 +22,19 @@ data(syn_data_tibble) test_data <- syn_data_tibble test_data -test_data_prepared <- prepare_input_regions( +test_data_prepared <- peakCombiner:::prepare_input_regions( data = test_data, show_messages = TRUE ) -test_data_center_expand <- center_expand_regions( +test_data_center_expand <- peakCombiner:::center_expand_regions( data = test_data_prepared, center_by = "center_column", expand_by = NULL, show_messages = TRUE ) -test_data_filtered <- filter_regions( +test_data_filtered <- peakCombiner:::filter_regions( data = test_data_center_expand, include_by_chromosome_name = NULL, exclude_by_blacklist = "hg38", # "hg38", @@ -41,7 +43,7 @@ test_data_filtered <- filter_regions( show_messages = TRUE ) -test_data_combined <- combine_regions( +test_data_combined <- peakCombiner:::combine_regions( data = test_data_filtered, combined_center = "nearest", annotate_with_input_names = FALSE, @@ -54,14 +56,14 @@ test_data_combined <- combine_regions( ### -----------------------------------------------------------------------### testthat::test_that("Input data frame has be data frame or tibble", { - testthat::expect_error(combine_regions( + testthat::expect_error(peakCombiner:::combine_regions( data = c(1, 2, 3, 4, 5), show_messages = FALSE )) }) testthat::test_that("Input data frame has be data frame or tibble", { - testthat::expect_error(combine_regions( + testthat::expect_error(peakCombiner:::combine_regions( data = NULL, show_messages = FALSE )) @@ -69,7 +71,7 @@ testthat::test_that("Input data frame has be data frame or tibble", { ### -----------------------------------------------------------------------### testthat::test_that("Argument 'combined_center' creates error if NULL", { - testthat::expect_error(combine_regions( + testthat::expect_error(peakCombiner:::combine_regions( data = test_data_filtered, combined_center = NULL, show_messages = FALSE @@ -77,7 +79,7 @@ testthat::test_that("Argument 'combined_center' creates error if NULL", { }) testthat::test_that("Argument 'combined_center' creates error if NA", { - testthat::expect_error(combine_regions( + testthat::expect_error(peakCombiner:::combine_regions( data = test_data_filtered, combined_center = NA, show_messages = FALSE @@ -86,7 +88,7 @@ testthat::test_that("Argument 'combined_center' creates error if NA", { testthat::test_that("Argument 'combined_center' creates error if numeric value", { - testthat::expect_error(combine_regions( + testthat::expect_error(peakCombiner:::combine_regions( data = test_data_filtered, combined_center = 1, show_messages = FALSE @@ -94,7 +96,7 @@ testthat::test_that("Argument 'combined_center' creates error if numeric }) testthat::test_that("Argument 'combined_center' tolerates capitilization", { - testthat::expect_no_error(combine_regions( + testthat::expect_no_error(peakCombiner:::combine_regions( data = test_data_filtered, combined_center = "Nearest", show_messages = FALSE @@ -103,7 +105,7 @@ testthat::test_that("Argument 'combined_center' tolerates capitilization", { testthat::test_that("Argument 'combined_center' creates error if not allowes value", { - testthat::expect_error(combine_regions( + testthat::expect_error(peakCombiner:::combine_regions( data = test_data_filtered, combined_center = "Shortest", show_messages = FALSE @@ -113,12 +115,12 @@ testthat::test_that("Argument 'combined_center' creates error if not allowes ### -----------------------------------------------------------------------### testthat::test_that("Argument 'annotate_with_input_names' creates no error if allowed value", { - testthat::expect_no_error(combine_regions( + testthat::expect_no_error(peakCombiner:::combine_regions( data = test_data_filtered, annotate_with_input_names = TRUE, show_messages = FALSE )) - testthat::expect_no_error(combine_regions( + testthat::expect_no_error(peakCombiner:::combine_regions( data = test_data_filtered, annotate_with_input_names = FALSE, show_messages = FALSE @@ -127,13 +129,13 @@ testthat::test_that("Argument 'annotate_with_input_names' creates no error if testthat::test_that("Argument 'annotate_with_input_names' creates error if not allowes value", { - testthat::expect_error(combine_regions( + testthat::expect_error(peakCombiner:::combine_regions( data = test_data_filtered, annotate_with_input_names = FALSe, show_messages = FALSE )) - testthat::expect_error(combine_regions( + testthat::expect_error(peakCombiner:::combine_regions( data = test_data_filtered, annotate_with_input_names = 10, show_messages = FALSE @@ -142,7 +144,7 @@ testthat::test_that("Argument 'annotate_with_input_names' creates error if not testthat::test_that("Argument 'annotate_with_input_names' creates error if not allowes value 'NA'", { - testthat::expect_error(combine_regions( + testthat::expect_error(peakCombiner:::combine_regions( data = test_data_filtered, annotate_with_input_names = NA, show_messages = FALSE @@ -151,7 +153,7 @@ testthat::test_that("Argument 'annotate_with_input_names' creates error if not testthat::test_that("Argument 'annotate_with_input_names' creates error if not allowes value 'NULL'", { - testthat::expect_error(combine_regions( + testthat::expect_error(peakCombiner:::combine_regions( data = test_data_filtered, annotate_with_input_names = NULL, show_messages = FALSE @@ -160,7 +162,7 @@ testthat::test_that("Argument 'annotate_with_input_names' creates error if not testthat::test_that("Argument 'annotate_with_input_names' creates error if length is greater then 1.", { - testthat::expect_error(combine_regions( + testthat::expect_error(peakCombiner:::combine_regions( data = test_data_filtered, annotate_with_input_names = c(1, 2), show_messages = FALSE @@ -169,7 +171,7 @@ testthat::test_that("Argument 'annotate_with_input_names' creates error if testthat::test_that("Argument 'annotate_with_input_names' creates error if not allowed logical value with length 2 is provided.", { - testthat::expect_error(combine_regions( + testthat::expect_error(peakCombiner:::combine_regions( data = test_data_filtered, annotate_with_input_names = c(NA, TRUE), show_messages = FALSE @@ -179,7 +181,7 @@ testthat::test_that("Argument 'annotate_with_input_names' creates error if not testthat::test_that("Argument 'combined_sample_name' creates no error if 'NULL' value is provided.", { - testthat::expect_no_error(combine_regions( + testthat::expect_no_error(peakCombiner:::combine_regions( data = test_data_filtered, combined_sample_name = NULL, show_messages = FALSE @@ -188,7 +190,7 @@ testthat::test_that("Argument 'combined_sample_name' creates no error if 'NULL' testthat::test_that("Argument 'combined_sample_name' creates no error if single character value is provided.", { - testthat::expect_no_error(combine_regions( + testthat::expect_no_error(peakCombiner:::combine_regions( data = test_data_filtered, combined_sample_name = "Consensus", show_messages = FALSE @@ -197,7 +199,7 @@ testthat::test_that("Argument 'combined_sample_name' creates no error if single testthat::test_that("Argument 'combined_sample_name' creates error if single numeric value is provided.", { - testthat::expect_error(combine_regions( + testthat::expect_error(peakCombiner:::combine_regions( data = test_data_filtered, combined_sample_name = 1, show_messages = FALSE @@ -206,7 +208,7 @@ testthat::test_that("Argument 'combined_sample_name' creates error if single testthat::test_that("Argument 'combined_sample_name' creates error if vector with two entries is provided.", { - testthat::expect_error(combine_regions( + testthat::expect_error(peakCombiner:::combine_regions( data = test_data_filtered, combined_sample_name = c("Consensus", "Two"), show_messages = FALSE @@ -215,7 +217,7 @@ testthat::test_that("Argument 'combined_sample_name' creates error if vector testthat::test_that("Argument 'combined_sample_name' creates error if 'NA' is provided.", { - testthat::expect_error(combine_regions( + testthat::expect_error(peakCombiner:::combine_regions( data = test_data_filtered, combined_sample_name = NA, show_messages = FALSE @@ -226,11 +228,11 @@ testthat::test_that("Argument 'combined_sample_name' creates error if 'NA' is testthat::test_that("Argument 'show_messages' creates no error if TRUE or FALSE value is provided.", { - testthat::expect_no_error(combine_regions( + testthat::expect_no_error(peakCombiner:::combine_regions( data = test_data_filtered, show_messages = FALSE )) - testthat::expect_no_error(combine_regions( + testthat::expect_no_error(peakCombiner:::combine_regions( data = test_data_filtered, show_messages = TRUE )) @@ -238,7 +240,7 @@ testthat::test_that("Argument 'show_messages' creates no error if TRUE or FALSE testthat::test_that("Argument 'show_messages' creates no error if non accepted value is provided.", { - testthat::expect_error(combine_regions( + testthat::expect_error(peakCombiner:::combine_regions( data = test_data_filtered, show_messages = FaLSE )) @@ -246,7 +248,7 @@ testthat::test_that("Argument 'show_messages' creates no error if non accepted testthat::test_that("Argument 'show_messages' creates no error if non accepted value 'NA' is provided.", { - testthat::expect_error(combine_regions( + testthat::expect_error(peakCombiner:::combine_regions( data = test_data_filtered, show_messages = NA )) @@ -278,7 +280,7 @@ testthat::test_that("Input data frame has the expected structure", { ### -----------------------------------------------------------------------### testthat::test_that("Output data has the correct classes and structure", { - testthat::expect_no_error(check_data_structure(test_data_combined)) + testthat::expect_no_error(peakCombiner:::check_data_structure(test_data_combined)) }) testthat::test_that("Output data frame has correct colnames", { @@ -290,7 +292,7 @@ testthat::test_that("Output data frame has correct colnames", { testthat::test_that("Output data results has correct summit for 'nearest' peak", { - data <- combine_regions( + data <- peakCombiner:::combine_regions( data = test_data_filtered, found_in_samples = 2, combined_center = "nearest", @@ -304,7 +306,7 @@ testthat::test_that("Output data results has correct summit for 'nearest' }) test_that("Output data results has correct summit for 'strongst' peak", { - data <- combine_regions( + data <- peakCombiner:::combine_regions( data = test_data_filtered, found_in_samples = 2, combined_center = "strongest", @@ -319,7 +321,7 @@ test_that("Output data results has correct summit for 'strongst' peak", { testthat::test_that("Output data results has correct summit for 'middle' peak", { - data <- combine_regions( + data <- peakCombiner:::combine_regions( data = test_data_filtered, found_in_samples = 2, combined_center = "middle", diff --git a/tests/testthat/test-cr_add_summit.R b/tests/testthat/test-cr_add_summit.R index 8d76baa..05bf2c6 100644 --- a/tests/testthat/test-cr_add_summit.R +++ b/tests/testthat/test-cr_add_summit.R @@ -3,6 +3,8 @@ ### Prepare data for testing ### -----------------------------------------------------------------------### ## +library(peakCombiner) +## set.seed(1234) ## input_colnames <- c( @@ -21,17 +23,17 @@ output_colnames <- c( data(syn_data_tibble) test_data <- syn_data_tibble ## -test_data_prepared <- prepare_input_regions( +test_data_prepared <- peakCombiner::prepare_input_regions( data = test_data ) -test_data_center_expand <- center_expand_regions( +test_data_center_expand <- peakCombiner::center_expand_regions( data = test_data_prepared, center_by = "center_column", expand_by = NULL ) -test_data_filtered <- filter_regions( +test_data_filtered <- peakCombiner::filter_regions( data = test_data_center_expand, exclude_by_blacklist = "hg38", include_by_chromosome_name = c("chr1", "chr10", "chr2", "chr42"), @@ -39,14 +41,14 @@ test_data_filtered <- filter_regions( include_top_n_scoring = NULL ) -test_data_disjoin_filter <- cr_disjoin_filter(data = test_data_filtered, found_in_samples = 2) -test_data_reduce <- cr_reduce(data = test_data_disjoin_filter) -test_data_overlap <- cr_overlap_with_summits( +test_data_disjoin_filter <- peakCombiner:::cr_disjoin_filter(data = test_data_filtered, found_in_samples = 2) +test_data_reduce <- peakCombiner:::cr_reduce(data = test_data_disjoin_filter) +test_data_overlap <- peakCombiner:::cr_overlap_with_summits( data = test_data_reduce, input = test_data_filtered ) ## -test_data_combined_with_summit <- cr_add_summit( +test_data_combined_with_summit <- peakCombiner:::cr_add_summit( data = test_data_overlap, input = test_data_filtered, combined_center = "nearest", @@ -90,38 +92,38 @@ test_that("Meta data frame has the expected structure", { }) ## test_that("Parameter 'center' has the expected structure", { - expect_no_error(cr_add_summit( + expect_no_error(peakCombiner:::cr_add_summit( data = test_data_overlap, input = test_data_filtered, combined_center = "STRONGEST" )) - expect_no_error(cr_add_summit( + expect_no_error(peakCombiner:::cr_add_summit( data = test_data_overlap, input = test_data_filtered, combined_center = "middle" )) ## - expect_error(cr_add_summit( + expect_error(peakCombiner:::cr_add_summit( data = test_data_overlap, input = test_data_filtered, combined_center = mean )) - expect_error(cr_add_summit( + expect_error(peakCombiner:::cr_add_summit( data = test_data_overlap, input = test_data_filtered, combined_center = 2 )) - expect_error(cr_add_summit( + expect_error(peakCombiner:::cr_add_summit( data = test_data_overlap, input = test_data_filtered, combined_center = c(1, 2, 3) ), "`") - expect_error(cr_add_summit( + expect_error(peakCombiner:::cr_add_summit( data = test_data_overlap, input = test_data_filtered, combined_center = NULL ), "`") - expect_error(cr_add_summit( + expect_error(peakCombiner:::cr_add_summit( data = test_data_overlap, input = test_data_filtered, combined_center = NA @@ -153,21 +155,21 @@ test_that("Output data frame is correct", { }) ## test_that("Output data results with different summits", { - data <- cr_add_summit( + data <- peakCombiner:::cr_add_summit( data = test_data_overlap, input = test_data_filtered, combined_center = "nearest" ) expect_identical(data$center[7], 500) ## - data <- cr_add_summit( + data <- peakCombiner:::cr_add_summit( data = test_data_overlap, input = test_data_filtered, combined_center = "strongest" ) expect_identical(data$center[7], 600) ## - data <- cr_add_summit( + data <- peakCombiner:::cr_add_summit( data = test_data_overlap, input = test_data_filtered, combined_center = "middle" diff --git a/tests/testthat/test-cr_disjoin_filter.R b/tests/testthat/test-cr_disjoin_filter.R index 878198e..d9ff790 100644 --- a/tests/testthat/test-cr_disjoin_filter.R +++ b/tests/testthat/test-cr_disjoin_filter.R @@ -3,6 +3,10 @@ ### Prepare data for testing ### -----------------------------------------------------------------------### ## +library(peakCombiner) +## +set.seed(1234) +## required_colnames <- c( "chrom", "start", "end", "name", "score", "strand", "center", "sample_name" ) @@ -11,15 +15,15 @@ data(syn_data_tibble) test_data <- syn_data_tibble input_colnames <- colnames(test_data) ## -test_data_prepared <- prepare_input_regions( +test_data_prepared <- peakCombiner::prepare_input_regions( data = test_data ) -test_data_center_expand <- center_expand_regions( +test_data_center_expand <- peakCombiner::center_expand_regions( data = test_data_prepared, center_by = "center_column", expand_by = NULL ) -test_data_filtered <- filter_regions( +test_data_filtered <- peakCombiner::filter_regions( data = test_data_center_expand, exclude_by_blacklist = "hg38", # "hg38", include_by_chromosome_name = NULL, @@ -28,7 +32,7 @@ test_data_filtered <- filter_regions( ) ## -test_data_disjoin_filter <- cr_disjoin_filter( +test_data_disjoin_filter <- peakCombiner:::cr_disjoin_filter( data = test_data_filtered, found_in_samples = 2 ) @@ -56,27 +60,27 @@ test_that("Input data frame has the expected structure", { }) ## test_that("Parameter 'found_in_samples' has the correct structure", { - expect_no_error(cr_disjoin_filter( + expect_no_error(peakCombiner:::cr_disjoin_filter( data = test_data_filtered, found_in_samples = 3 )) - expect_error(cr_disjoin_filter( + expect_error(peakCombiner:::cr_disjoin_filter( data = test_data_filtered, found_in_samples = 0 ), "Arg") - expect_error(cr_disjoin_filter( + expect_error(peakCombiner:::cr_disjoin_filter( data = test_data_filtered, found_in_samples = NULL ), "Arg") - expect_error(cr_disjoin_filter( + expect_error(peakCombiner:::cr_disjoin_filter( data = test_data_filtered, found_in_samples = NA ), ) - expect_error(cr_disjoin_filter( + expect_error(peakCombiner:::cr_disjoin_filter( data = test_data_filtered, found_in_samples = c(1, 2, 3) ), "'") - expect_error(cr_disjoin_filter( + expect_error(peakCombiner:::cr_disjoin_filter( data = test_data_filtered, found_in_samples = test_data_filtered ), "Arg") diff --git a/tests/testthat/test-cr_overlap_with_summits.R b/tests/testthat/test-cr_overlap_with_summits.R index db06807..115dab7 100644 --- a/tests/testthat/test-cr_overlap_with_summits.R +++ b/tests/testthat/test-cr_overlap_with_summits.R @@ -3,6 +3,10 @@ ### Prepare data for testing ### -----------------------------------------------------------------------### ## +library(peakCombiner) +## +set.seed(1234) +## reduced_colnames <- c( "chrom", "start", "end", "width", "strand", "name", "center", "score" ) @@ -19,30 +23,30 @@ data(syn_data_tibble) test_data <- syn_data_tibble input_colnames <- colnames(test_data) ## -test_data_prepared <- prepare_input_regions( +test_data_prepared <- peakCombiner::prepare_input_regions( data = test_data ) -test_data_center_expand <- center_expand_regions( +test_data_center_expand <- peakCombiner::center_expand_regions( data = test_data_prepared, center_by = "center_column", expand_by = NULL ) -test_data_filtered <- filter_regions( +test_data_filtered <- peakCombiner::filter_regions( data = test_data_center_expand, exclude_by_blacklist = "hg38", include_by_chromosome_name = c("chr1", "chr10", "chr2", "chr42"), include_above_score_cutoff = NULL, include_top_n_scoring = NULL ) -test_data_disjoin_filter <- cr_disjoin_filter( +test_data_disjoin_filter <- peakCombiner:::cr_disjoin_filter( data = test_data_filtered, found_in_samples = 2 ) -test_data_reduce <- cr_reduce( +test_data_reduce <- peakCombiner:::cr_reduce( data = test_data_disjoin_filter ) ## -test_data_overlap <- cr_overlap_with_summits( +test_data_overlap <- peakCombiner:::cr_overlap_with_summits( data = test_data_reduce, input = test_data_filtered ) diff --git a/tests/testthat/test-cr_reduce.R b/tests/testthat/test-cr_reduce.R index f4b43e1..1640a16 100644 --- a/tests/testthat/test-cr_reduce.R +++ b/tests/testthat/test-cr_reduce.R @@ -3,6 +3,8 @@ ### Prepare data for testing ### -----------------------------------------------------------------------### ## +library(peakCombiner) +## set.seed(1234) ## input_colnames <- c( @@ -15,17 +17,17 @@ output_colnames <- c("chr", "start", "end", "width", "strand", "input_names") data(syn_data_tibble) test_data <- syn_data_tibble ## -test_data_prepared <- prepare_input_regions( +test_data_prepared <- peakCombiner::prepare_input_regions( data = test_data ) ## -test_data_center_expand <- center_expand_regions( +test_data_center_expand <- peakCombiner::center_expand_regions( data = test_data_prepared, center_by = "center_column", expand_by = NULL ) ## -test_data_filtered <- filter_regions( +test_data_filtered <- peakCombiner::filter_regions( data = test_data_center_expand, exclude_by_blacklist = "hg38", include_by_chromosome_name = c("chr1", "chr10", "chr2", "chr42"), @@ -33,12 +35,12 @@ test_data_filtered <- filter_regions( include_top_n_scoring = NULL ) ## -test_data_disjoin_filter <- cr_disjoin_filter( +test_data_disjoin_filter <- peakCombiner:::cr_disjoin_filter( data = test_data_filtered, found_in_samples = 2 ) ## -test_data_reduce <- cr_reduce( +test_data_reduce <- peakCombiner:::cr_reduce( data = test_data_disjoin_filter ) ## diff --git a/tests/testthat/test-define_expansion.R b/tests/testthat/test-define_expansion.R index c2ba051..19fcbe5 100644 --- a/tests/testthat/test-define_expansion.R +++ b/tests/testthat/test-define_expansion.R @@ -3,6 +3,10 @@ ### Prepare data for testing ### -----------------------------------------------------------------------### ## +library(peakCombiner) +## +set.seed(123) +## required_colnames <- c( "chrom", "start", "end", "name", "score", "strand", "center", "sample_name" @@ -14,7 +18,7 @@ data(syn_data_tibble) test_data <- syn_data_tibble input_colnames <- colnames(test_data) ## -test_data_prepared <- prepare_input_regions( +test_data_prepared <- peakCombiner::prepare_input_regions( data = test_data ) ## diff --git a/tests/testthat/test-filter_by_blacklist.R b/tests/testthat/test-filter_by_blacklist.R index 481db57..a57f281 100644 --- a/tests/testthat/test-filter_by_blacklist.R +++ b/tests/testthat/test-filter_by_blacklist.R @@ -3,6 +3,8 @@ ### Prepare data for testing ### -----------------------------------------------------------------------### ## +library(peakCombiner) +## set.seed(1234) ## required_colnames <- c( @@ -14,17 +16,17 @@ data(syn_data_tibble) test_data <- syn_data_tibble input_colnames <- colnames(test_data) ## -test_data_prepared <- prepare_input_regions( +test_data_prepared <- peakCombiner::prepare_input_regions( data = test_data ) ## -test_data_center_expand <- center_expand_regions( +test_data_center_expand <- peakCombiner::center_expand_regions( data = test_data_prepared, center_by = "center_column", expand_by = NULL ) ## -test_data_filtered <- filter_by_chromosome_names( +test_data_filtered <- peakCombiner::filter_by_chromosome_names( data = test_data_center_expand, include_by_chromosome_name = c("chr1", "chr10", "chr42") ) @@ -34,7 +36,7 @@ input_colnames <- colnames(test_data_filtered) data(blacklist_hg38) blacklist <- blacklist_hg38 ## -test_data_filtered_bl <- filter_by_blacklist( +test_data_filtered_bl <- peakCombiner:::filter_by_blacklist( data = test_data_filtered, exclude_by_blacklist = blacklist ) @@ -47,15 +49,15 @@ result_colnames <- colnames(test_data_filtered) ## ## test_that("Test if function works with correct input", { - expect_no_error(filter_by_blacklist( + expect_no_error(peakCombiner:::filter_by_blacklist( data = test_data_filtered, exclude_by_blacklist = blacklist )) - expect_no_error(filter_by_blacklist( + expect_no_error(peakCombiner:::filter_by_blacklist( data = test_data_filtered, exclude_by_blacklist = NULL )) - expect_no_error(filter_by_blacklist( + expect_no_error(peakCombiner:::filter_by_blacklist( data = test_data_filtered, exclude_by_blacklist = "hg38" )) @@ -82,20 +84,20 @@ test_that("Input data frame has the expected structure", { ### -----------------------------------------------------------------------### ## test_that("Required parameter 'filter_by_blacklist' has expected structure", { - expect_no_error(filter_by_blacklist( + expect_no_error(peakCombiner:::filter_by_blacklist( data = test_data_filtered, exclude_by_blacklist = NULL )) - expect_no_error(filter_by_blacklist( + expect_no_error(peakCombiner:::filter_by_blacklist( data = test_data_filtered, exclude_by_blacklist = "HG38" )) - expect_no_error(filter_by_blacklist( + expect_no_error(peakCombiner:::filter_by_blacklist( data = test_data_filtered, exclude_by_blacklist = "mm10" )) ## - expect_error(filter_by_blacklist( + expect_error(peakCombiner:::filter_by_blacklist( data = test_data_filtered, filter_by_blacklist = blacklist[1:2] )) @@ -108,14 +110,14 @@ test_that("For 'filter_by_blacklist' providing blacklist with different blacklist2 <- blacklist colnames(blacklist2) <- c("CHROM", "start", "end") ## - expect_no_error(filter_by_blacklist( + expect_no_error(peakCombiner:::filter_by_blacklist( data = test_data_filtered, exclude_by_blacklist = blacklist2 )) ## colnames(blacklist2) <- c("seqnames", "start", "end") ## - expect_error(filter_by_blacklist( + expect_error(peakCombiner:::filter_by_blacklist( data = test_data_filtered, exclude_by_blacklist = blacklist2 )) @@ -124,19 +126,19 @@ test_that("For 'filter_by_blacklist' providing blacklist with different ### -----------------------------------------------------------------------### ## test_that("Wrong input for exclude_by_blacklist for 'filter_by_blacklist'", { - expect_error(filter_by_blacklist( + expect_error(peakCombiner:::filter_by_blacklist( data = test_data_filtered, exclude_by_blacklist = "mm38" )) - expect_error(filter_by_blacklist( + expect_error(peakCombiner:::filter_by_blacklist( data = test_data_filtered, exclude_by_blacklist = hg38 )) - expect_error(filter_by_blacklist( + expect_error(peakCombiner:::filter_by_blacklist( data = test_data_filtered, exclude_by_blacklist = 1 )) - expect_error(filter_by_blacklist( + expect_error(peakCombiner:::filter_by_blacklist( data = test_data_filtered, exclude_by_blacklist = c(1, 2) )) diff --git a/tests/testthat/test-filter_by_chromosome_names.R b/tests/testthat/test-filter_by_chromosome_names.R index 5964304..4f49a35 100644 --- a/tests/testthat/test-filter_by_chromosome_names.R +++ b/tests/testthat/test-filter_by_chromosome_names.R @@ -3,6 +3,8 @@ ### Prepare data for testing ### -----------------------------------------------------------------------### ## +library(peakCombiner) +## set.seed(1234) ## required_colnames <- c( @@ -14,11 +16,11 @@ data(syn_data_tibble) test_data <- syn_data_tibble input_colnames <- colnames(test_data) ## -test_data_prepared <- prepare_input_regions( +test_data_prepared <- peakCombiner::prepare_input_regions( data = test_data ) ## -test_data_center_expand <- center_expand_regions( +test_data_center_expand <- peakCombiner::center_expand_regions( data = test_data_prepared, center_by = "center_column", expand_by = NULL @@ -28,7 +30,7 @@ input_colnames <- colnames(test_data_center_expand) ## keep_chromosomes <- c("chr1", "chr10", "chr42") ## -test_data_filtered <- filter_by_chromosome_names( +test_data_filtered <- peakCombiner:::filter_by_chromosome_names( data = test_data_center_expand, include_by_chromosome_name = keep_chromosomes ) @@ -40,7 +42,7 @@ result_colnames <- colnames(test_data_filtered) ### -----------------------------------------------------------------------### ## test_that("Test if function works with correct input", { - expect_no_error(filter_by_chromosome_names( + expect_no_error(peakCombiner:::filter_by_chromosome_names( data = test_data_center_expand, include_by_chromosome_name = keep_chromosomes )) @@ -68,20 +70,20 @@ test_that("Input data frame has the expected structure", { ## test_that("Required parameter 'filter_by_chromosome_names' has expected structure", { - expect_no_error(filter_by_chromosome_names( + expect_no_error(peakCombiner:::filter_by_chromosome_names( data = test_data_filtered, include_by_chromosome_name = NULL )) - expect_no_error(filter_by_chromosome_names( + expect_no_error(peakCombiner:::filter_by_chromosome_names( data = test_data_filtered, include_by_chromosome_name = "chr1" )) - expect_no_error(filter_by_chromosome_names( + expect_no_error(peakCombiner:::filter_by_chromosome_names( data = test_data_filtered, include_by_chromosome_name = keep_chromosomes )) ## - expect_error(filter_by_chromosome_names( + expect_error(peakCombiner:::filter_by_chromosome_names( data = test_data_filtered, include_by_chromosome_name = NA )) diff --git a/tests/testthat/test-filter_by_significance.R b/tests/testthat/test-filter_by_significance.R index 5e6fb60..ca4381b 100644 --- a/tests/testthat/test-filter_by_significance.R +++ b/tests/testthat/test-filter_by_significance.R @@ -3,6 +3,8 @@ ### Prepare data for testing ### -----------------------------------------------------------------------### ## +library(peakCombiner) +## set.seed(1234) ## required_colnames <- c( @@ -14,10 +16,10 @@ data(syn_data_tibble) test_data <- syn_data_tibble input_colnames <- colnames(test_data) ## -test_data_prepared <- prepare_input_regions( +test_data_prepared <- peakCombiner::prepare_input_regions( data = test_data ) -test_data_center_expand <- center_expand_regions( +test_data_center_expand <- peakCombiner::center_expand_regions( data = test_data_prepared, center_by = "center_column", expand_by = NULL @@ -27,7 +29,7 @@ input_colnames <- colnames(test_data_center_expand) ## filter_by_significance <- 40 ## -test_data_filtered <- filter_by_significance( +test_data_filtered <- peakCombiner:::filter_by_significance( data = test_data_center_expand, include_above_score_cutoff = filter_by_significance ) @@ -39,7 +41,7 @@ result_colnames <- colnames(test_data_filtered) ### -----------------------------------------------------------------------### ## test_that("Test if function works with correct input", { - expect_no_error(filter_by_significance( + expect_no_error(peakCombiner:::filter_by_significance( data = test_data_center_expand, include_above_score_cutoff = filter_by_significance )) @@ -66,24 +68,24 @@ test_that("Input data frame has the expected structure", { ### -----------------------------------------------------------------------### ## test_that("Required parameter 'filter_by_significance' has expected structure", { - expect_no_error(filter_by_significance( + expect_no_error(peakCombiner:::filter_by_significance( data = test_data_filtered, include_above_score_cutoff = NULL )) - expect_no_error(filter_by_significance( + expect_no_error(peakCombiner:::filter_by_significance( data = test_data_filtered, include_above_score_cutoff = 0 )) ## - expect_error(filter_by_significance( + expect_error(peakCombiner:::filter_by_significance( data = test_data_filtered, include_above_score_cutoff = NA )) - expect_error(filter_by_significance( + expect_error(peakCombiner:::filter_by_significance( data = test_data_filtered, include_above_score_cutoff = "nonexisting" )) - expect_error(filter_by_significance( + expect_error(peakCombiner:::filter_by_significance( data = test_data_filtered, include_above_score_cutoff = c(1, 2, 3) )) diff --git a/tests/testthat/test-filter_by_top_enriched.R b/tests/testthat/test-filter_by_top_enriched.R index 68ec897..c287e79 100644 --- a/tests/testthat/test-filter_by_top_enriched.R +++ b/tests/testthat/test-filter_by_top_enriched.R @@ -3,6 +3,8 @@ ### Prepare data for testing ### -----------------------------------------------------------------------### ## +library(peakCombiner) +## set.seed(1234) ## required_colnames <- c( @@ -14,10 +16,10 @@ data(syn_data_tibble) test_data <- syn_data_tibble input_colnames <- colnames(test_data) ## -test_data_prepared <- prepare_input_regions( +test_data_prepared <- peakCombiner::prepare_input_regions( data = test_data ) -test_data_center_expand <- center_expand_regions( +test_data_center_expand <- peakCombiner::center_expand_regions( data = test_data_prepared, center_by = "center_column", expand_by = NULL @@ -25,7 +27,7 @@ test_data_center_expand <- center_expand_regions( ## input_colnames <- colnames(test_data_center_expand) ## -test_data_filtered <- filter_by_top_enriched( +test_data_filtered <- peakCombiner:::filter_by_top_enriched( data = test_data_center_expand, include_top_n_scoring = 10 ) @@ -39,7 +41,7 @@ table(test_data_filtered$sample_name) ### -----------------------------------------------------------------------### ## test_that("Test if function works with correct input", { - expect_no_error(filter_by_top_enriched( + expect_no_error(peakCombiner:::filter_by_top_enriched( data = test_data_center_expand, include_top_n_scoring = 10 )) @@ -66,28 +68,28 @@ test_that("Input data frame has the expected structure", { ### -----------------------------------------------------------------------### ## test_that("Required parameter 'filter_by_top_enriched' has expected structure", { - expect_no_error(filter_by_top_enriched( + expect_no_error(peakCombiner:::filter_by_top_enriched( data = test_data_center_expand, include_top_n_scoring = NULL )) - expect_no_error(filter_by_top_enriched( + expect_no_error(peakCombiner:::filter_by_top_enriched( data = test_data_center_expand, include_top_n_scoring = 5 )) ## - expect_error(filter_by_top_enriched( + expect_error(peakCombiner:::filter_by_top_enriched( data = test_data_center_expand, include_top_n_scoring = 0 )) - expect_error(filter_by_top_enriched( + expect_error(peakCombiner:::filter_by_top_enriched( data = test_data_center_expand, include_top_n_scoring = NA )) - expect_error(filter_by_top_enriched( + expect_error(peakCombiner:::filter_by_top_enriched( data = test_data_center_expand, include_top_n_scoring = "notexisting" )) - expect_error(filter_by_top_enriched( + expect_error(peakCombiner:::filter_by_top_enriched( data = test_data_center_expand, include_top_n_scoring = c(1, 2, 3) )) diff --git a/tests/testthat/test-filter_regions.R b/tests/testthat/test-filter_regions.R index bbf8218..9f4eb3e 100644 --- a/tests/testthat/test-filter_regions.R +++ b/tests/testthat/test-filter_regions.R @@ -3,6 +3,7 @@ ### Prepare data for testing ### -----------------------------------------------------------------------### ## +library(peakCombiner) set.seed(1234) ## required_colnames <- c( @@ -15,10 +16,10 @@ test_data <- syn_data_tibble input_colnames <- colnames(test_data) ## -test_data_prepared <- prepare_input_regions( +test_data_prepared <- peakCombiner::prepare_input_regions( data = test_data ) -test_data_center_expand <- center_expand_regions( +test_data_center_expand <- peakCombiner::center_expand_regions( data = test_data_prepared, center_by = "center_column", expand_by = NULL @@ -26,7 +27,7 @@ test_data_center_expand <- center_expand_regions( ## input_colnames <- colnames(test_data_center_expand) ## -test_data_filtered <- filter_regions( +test_data_filtered <- peakCombiner::filter_regions( data = test_data_center_expand, include_by_chromosome_name = NULL, exclude_by_blacklist = "hg38", @@ -36,13 +37,13 @@ test_data_filtered <- filter_regions( ## result_colnames <- colnames(test_data_filtered) ## -test_data_combined <- combine_regions( +test_data_combined <- peakCombiner::combine_regions( data = test_data_filtered, found_in_samples = 2, combined_center = "nearest" ) ## -test_data_combined_ce <- center_expand_regions( +test_data_combined_ce <- peakCombiner::center_expand_regions( data = test_data_combined, center_by = "center_column", expand_by = NULL @@ -107,7 +108,7 @@ test_that("Output data frame is correct for data_prepared", { ## data <- test_data_prepared ## - expect_no_error(filter_regions( + expect_no_error(peakCombiner::filter_regions( data = data, exclude_by_blacklist = "hg38", include_by_chromosome_name = NULL, @@ -115,7 +116,7 @@ test_that("Output data frame is correct for data_prepared", { include_top_n_scoring = NULL )) ## - result <- filter_regions( + result <- peakCombiner::filter_regions( data = data, exclude_by_blacklist = "hg38", include_by_chromosome_name = NULL, @@ -131,7 +132,7 @@ test_that("Output data frame is correct for data_center_expand", { ## data <- test_data_center_expand ## - result <- filter_regions( + result <- peakCombiner::filter_regions( data = data, exclude_by_blacklist = "hg38", include_by_chromosome_name = NULL, @@ -146,7 +147,7 @@ test_that("Output data frame is correct for data_center_expand", { test_that("Output data frame is correct for data_filtered", { ## data <- test_data_filtered - result <- filter_regions( + result <- peakCombiner::filter_regions( data = data, exclude_by_blacklist = "hg38", include_by_chromosome_name = NULL, @@ -161,7 +162,7 @@ test_that("Output data frame is correct for data_filtered", { test_that("Output data frame is correct for data_combined", { ## data <- test_data_combined - result <- filter_regions( + result <- peakCombiner::filter_regions( data = data, exclude_by_blacklist = "hg38", include_by_chromosome_name = NULL, @@ -176,7 +177,7 @@ test_that("Output data frame is correct for data_combined", { test_that("Output data frame is correct for data_combined_ce", { ## data <- test_data_combined_ce - result <- filter_regions( + result <- peakCombiner::filter_regions( data = data, exclude_by_blacklist = "hg38", include_by_chromosome_name = NULL, diff --git a/tests/testthat/test-load_input_regions.R b/tests/testthat/test-load_input_regions.R index f758158..53b7db3 100644 --- a/tests/testthat/test-load_input_regions.R +++ b/tests/testthat/test-load_input_regions.R @@ -3,6 +3,8 @@ ### Prepare data for testing ### -----------------------------------------------------------------------### ## +library(peakCombiner) +## data(syn_data_tibble) test_data <- syn_data_tibble ## @@ -20,7 +22,7 @@ data_prepared <- test_data ### -----------------------------------------------------------------------### ## test_that("Test if function works with correct input", { - expect_error(load_input_regions( + expect_error(peakCombiner::load_input_regions( data = test_data )) }) @@ -54,31 +56,31 @@ test_that("Input column 'sample_name' is a class 'character'.", { ### -----------------------------------------------------------------------### ## test_that("Error occurs when 'data' does not exist.", { - expect_error(load_input_regions( + expect_error(peakCombiner::load_input_regions( data = "nonexisting" ), ) }) ## test_that("Error occurs when 'data' has the wrong structure.", { - expect_error(load_input_regions( + expect_error(peakCombiner::load_input_regions( data = tibble(1:10) )) }) ## test_that("Error occurs when 'data' is a vector.", { - expect_error(load_input_regions( + expect_error(peakCombiner::load_input_regions( data = as.vector(1:10) ), ) }) ## test_that("Error occurs when 'data' is 'NULL'.", { - expect_error(load_input_regions( + expect_error(peakCombiner::load_input_regions( data = NULL ), ) }) ## test_that("Error occurs when 'data' is 'NA'.", { - expect_error(load_input_regions( + expect_error(peakCombiner::load_input_regions( data = NA ), ) }) diff --git a/tests/testthat/test-prepare_input_regions.R b/tests/testthat/test-prepare_input_regions.R index df51be3..a73a30f 100644 --- a/tests/testthat/test-prepare_input_regions.R +++ b/tests/testthat/test-prepare_input_regions.R @@ -3,6 +3,8 @@ ### Prepare data for testing ### -----------------------------------------------------------------------### ## +library(peakCombiner) +## set.seed(1234) @@ -16,7 +18,7 @@ allowed_file_format <- c("narrowpeak", "broadpeak", "bed") data(syn_data_bed) samplesheet_test <- syn_data_bed -test_sample_sheet <- prepare_input_regions( +test_sample_sheet <- peakCombiner::prepare_input_regions( data = samplesheet_test[1, ] ) @@ -24,7 +26,7 @@ data(syn_data_tibble) test_data <- syn_data_tibble input_colnames <- colnames(test_data) -test_data_prepared <- prepare_input_regions( +test_data_prepared <- peakCombiner::prepare_input_regions( data = test_data ) @@ -35,7 +37,7 @@ restult_colnames <- colnames(test_data_prepared) ### -----------------------------------------------------------------------### ### Test pre-loaded data frame test_that("Test if function works with correct input", { - expect_no_error(prepare_input_regions( + expect_no_error(peakCombiner::prepare_input_regions( data = test_data )) }) @@ -89,7 +91,7 @@ test_that("Input column 'sample_name' is a class 'character'.", { ### -----------------------------------------------------------------------### test_that("Output data frame has the correct structure.", { - expect_no_error(check_data_structure(test_data_prepared)) + expect_no_error(peakCombiner::check_data_structure(test_data_prepared)) }) test_that("Column names of output data are identical with required once.", {