tests/testthat/test_tumorcomparer.R
In cannin/tumorcomparer: Compare Patient Samples to Cell Line Models Using Molecular Data and Weighted Similarity
# All tests are done on files in package using system.file()
test_that("sanity_check", {
expect_equal(2 * 2, 4)
})
# TODO Add tests
# test_that("plot_mds", {
# expect_equal(TRUE, FALSE)
# })
# test_that("run_shiny_app", {
# expect_equal(TRUE, TRUE)
# })
test_that("test_tar_working", {
# Constructing the example tar.gz file
# tar cvzf inst/extdata/mock_5_data_types.tar.gz ./inst/extdata/mock_5_data_types
tmp_dir <- tempdir()
# The example file should exist
test_file <- system.file('extdata/mock_5_data_types.tar.gz', package="tumorcomparer")
expect_true(file.exists(test_file))
# The compressed file should have files inside
files <- untar(test_file, list=TRUE)
files
expect_true(length(files) > 2)
# The uncompressed file should have multiple lines in it
untar(test_file, exdir=tmp_dir)
tmp_file <- file.path(tmp_dir, files[2])
expect_true(length(readLines(tmp_file)) > 2)
})
test_that("return_first_part", {
tmp <- return_first_part("22RV1_PROSTRATE")
expect_equal(tmp, "22RV1")
})
test_that("keep_only_high_level_cnas", {
set.seed(1)
tmp <- sample(c(-2, -1, 0, 1, 2), 100, replace=TRUE)
mat <- matrix(tmp, 10, 10)
results <- as.vector(keep_only_high_level_cnas(cna_mat=mat))
expect_false(any(results == 1 | results == -1))
})
test_that("keep_only_high_level_cnas", {
t1 <- as.matrix(c(1,1,1,1,1,1,2,2,2,3,3,3,4,4))
t2 <- as.matrix(rev(t1))
weight <- c(.5,.5,.5,.5,.5,1,1,1,1,2,2,2,2,2)
results <- calc_weighted_corr(t1, t2, weight)
expect_equal(results, matrix(-0.8108894, 1, 1))
})
test_that("compute_freq_alt", {
set.seed(1)
tmp <- sample(c(0, 1), 100, replace=TRUE)
mat <- matrix(tmp, 10, 10)
expect_equal(0.51, compute_freq_alt(mat))
})
test_that("categorize_cell_lines", {
comparison_result <- readRDS(system.file("test_output", "ov_comparison_result.rds", package="tumorcomparer"))
categorization_list <- categorize_cell_lines(
num_tumors_for_comparison=length(comparison_result$tumor_ids)-1,
dist_mat=comparison_result$dist_mat,
cell_line_ids=comparison_result$cell_line_ids,
tumor_ids=comparison_result$tumor_ids,
trim_cell_line_names=FALSE)
expect_equal(categorization_list$categorization$Sample_ID[c(1,6,13)], c("OAW-28", "OV-17R", "OVK-18"))
expect_equal(categorization_list$categorization$Category[c(1,6,13)], c("Moderately Good", "Poor", "Outlier"))
})
test_that("generate_composite_mat_and_gene_weights", {
mut_default_weight <- 0.01
tumor_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_mut.txt", package="tumorcomparer")
cell_line_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_mut.txt", package="tumorcomparer")
known_cancer_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_mut.txt", package="tumorcomparer")
cancer_specific_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_mut.txt", package="tumorcomparer")
composite_mat <- generate_composite_mat_and_gene_weights(
default_weight=mut_default_weight,
tumor_file=tumor_mut_file,
cell_line_file=cell_line_mut_file,
known_cancer_gene_weights_file=known_cancer_gene_weights_mut_file,
cancer_specific_gene_weights_file=cancer_specific_gene_weights_mut_file)
#saveRDS(composite_mat, "inst/test_output/ov_composite_mat.rds")
#x <- readRDS("inst/test_output/ov_composite_mat.rds")
#expect_equal(composite_mat, x, tolerance = 0.001)
saved_output <- readRDS(system.file("test_output", "ov_composite_mat.rds", package="tumorcomparer"))
expect_equal(composite_mat, saved_output, tolerance = 0.001)
})
test_that("map_mean_similarity_to_gradient", {
comparison_result <- readRDS(system.file("test_output", "ov_comparison_result.rds", package="tumorcomparer"))
categorization_list <- categorize_cell_lines(
num_tumors_for_comparison=length(comparison_result$tumor_ids)-1,
dist_mat=comparison_result$dist_mat,
cell_line_ids=comparison_result$cell_line_ids,
tumor_ids=comparison_result$tumor_ids,
trim_cell_line_names=FALSE)
result <- map_mean_similarity_to_gradient(
mean_similarity_cell_line_to_k_nearest_tumors=categorization_list$mean_similarity_cell_line_to_k_nearest_tumors,
mean_similarity_tumor_to_k_nearest_tumors=categorization_list$mean_similarity_tumor_to_k_nearest_tumors,
col1="orange",
col2="blue",
numshades=100)
expect_equal(result[1:3], c("#DD8F21", "#F9A105", "#C37E3B"))
})
test_that("pair_dist", {
set.seed(1)
n <- 100
x <- sample(c(0, 1), n, replace=TRUE)
y <- sample(c(0, 1), n, replace=TRUE)
weights <- rnorm(n)
result <- pair_dist(x, y, weights)
expect_equal(result, 2.398, tolerance = 0.01)
})
test_that("run_comparison", {
set.seed(1)
tumor_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_mut.txt", package="tumorcomparer")
tumor_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_cna.txt", package="tumorcomparer")
tumor_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_exp.txt", package="tumorcomparer")
cell_line_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_mut.txt", package="tumorcomparer")
cell_line_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_cna.txt", package="tumorcomparer")
cell_line_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_exp.txt", package="tumorcomparer")
known_cancer_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_mut.txt", package="tumorcomparer")
known_cancer_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_cna.txt", package="tumorcomparer")
known_cancer_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_exp.txt", package="tumorcomparer")
cancer_specific_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_mut.txt", package="tumorcomparer")
cancer_specific_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_cna.txt", package="tumorcomparer")
cancer_specific_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_exp.txt", package="tumorcomparer")
comparison_result <- run_comparison(
available_data_types=c("mut", "cna", "exp"),
mut_data_type_weight = 1/3,
cna_data_type_weight = 1/3,
exp_data_type_weight = 1/3,
cna_default_weight=0.01,
mut_default_weight=0.01,
exp_default_weight=0.01,
tumor_mut_file=tumor_mut_file,
tumor_cna_file=tumor_cna_file,
tumor_exp_file=tumor_exp_file,
cell_line_mut_file=cell_line_mut_file,
cell_line_cna_file=cell_line_cna_file,
cell_line_exp_file=cell_line_exp_file,
known_cancer_gene_weights_mut_file=known_cancer_gene_weights_mut_file,
known_cancer_gene_weights_cna_file=known_cancer_gene_weights_cna_file,
known_cancer_gene_weights_exp_file=known_cancer_gene_weights_exp_file,
cancer_specific_gene_weights_mut_file=cancer_specific_gene_weights_mut_file,
cancer_specific_gene_weights_cna_file=cancer_specific_gene_weights_cna_file,
cancer_specific_gene_weights_exp_file=cancer_specific_gene_weights_exp_file)
#saveRDS(comparison_result, "inst/test_output/ov_comparison_result.rds")
#x <- readRDS("inst/test_output/ov_comparison_result.rds")
#expect_equal(comparison_result, x, tolerance = 0.001)
saved_output <- readRDS(system.file("test_output", "ov_comparison_result.rds", package="tumorcomparer"))
expect_equal(comparison_result, saved_output)
})
### test function on 3 data types for new generilized function
test_that("run_comparison_config_list", {
set.seed(1)
tumor_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_mut.txt", package="tumorcomparer")
tumor_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_cna.txt", package="tumorcomparer")
tumor_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_exp.txt", package="tumorcomparer")
cell_line_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_mut.txt", package="tumorcomparer")
cell_line_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_cna.txt", package="tumorcomparer")
cell_line_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_exp.txt", package="tumorcomparer")
known_cancer_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_mut.txt", package="tumorcomparer")
known_cancer_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_cna.txt", package="tumorcomparer")
known_cancer_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_exp.txt", package="tumorcomparer")
cancer_specific_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_mut.txt", package="tumorcomparer")
cancer_specific_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_cna.txt", package="tumorcomparer")
cancer_specific_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_exp.txt", package="tumorcomparer")
### creating config list for comparison function
config_list <- list(mut=list(dataset_name = "mut", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_mut_file, cell_line_file = cell_line_mut_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_mut_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_mut_file),
cna=list(dataset_name = "cna", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_cna_file, cell_line_file = cell_line_cna_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_cna_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_cna_file),
exp=list(dataset_name = "exp", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_exp_file, cell_line_file = cell_line_exp_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_exp_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_exp_file)
)
comparison_result <- run_comparison_config_list(config_list = config_list)
#saveRDS(comparison_result, "inst/test_output/comparison_config.rds")
#x <- readRDS("inst/test_output/comparison_config.rds")
#expect_equal(comparison_result, x, tolerance = 0.001)
saved_output <- readRDS(system.file("test_output", "comparison_config.rds", package="tumorcomparer"))
expect_equal(comparison_result, saved_output)
})
test_that("run_comparison_two_datasets", {
set.seed(1)
tumor_mut_file <- system.file("extdata", "READ_data_for_running_TC", "tumor_mut.txt", package="tumorcomparer")
tumor_exp_file <- system.file("extdata", "READ_data_for_running_TC", "tumor_exp.txt", package="tumorcomparer")
cell_line_mut_file <- system.file("extdata", "READ_data_for_running_TC", "cell_line_mut.txt", package="tumorcomparer")
cell_line_exp_file <- system.file("extdata", "READ_data_for_running_TC", "cell_line_exp.txt", package="tumorcomparer")
known_cancer_gene_weights_mut_file <- system.file("extdata", "READ_data_for_running_TC", "default_weights_for_known_cancer_genes_mut.txt", package="tumorcomparer")
known_cancer_gene_weights_exp_file <- system.file("extdata", "READ_data_for_running_TC", "default_weights_for_known_cancer_genes_exp.txt", package="tumorcomparer")
cancer_specific_gene_weights_mut_file <- system.file("extdata", "READ_data_for_running_TC", "Genes_and_weights_mut.txt", package="tumorcomparer")
cancer_specific_gene_weights_exp_file <- system.file("extdata", "READ_data_for_running_TC", "Genes_and_weights_exp.txt", package="tumorcomparer")
comparison_result <- run_comparison(
available_data_types=c("mut", "exp"),
mut_data_type_weight = 1/2,
exp_data_type_weight = 1/2,
cna_default_weight=0.01,
exp_default_weight=0.01,
tumor_mut_file=tumor_mut_file,
tumor_exp_file=tumor_exp_file,
cell_line_mut_file=cell_line_mut_file,
cell_line_exp_file=cell_line_exp_file,
known_cancer_gene_weights_mut_file=known_cancer_gene_weights_mut_file,
known_cancer_gene_weights_exp_file=known_cancer_gene_weights_exp_file,
cancer_specific_gene_weights_mut_file=cancer_specific_gene_weights_mut_file,
cancer_specific_gene_weights_exp_file=cancer_specific_gene_weights_exp_file)
#saveRDS(comparison_result, "inst/test_output/comparison_2_datasets.rds")
#x <- readRDS("inst/test_output/comparison_2_datasets.rds")
#expect_equal(comparison_result, x, tolerance = 0.001)
saved_output <- readRDS(system.file("test_output", "comparison_2_datasets.rds", package="tumorcomparer"))
expect_equal(comparison_result, saved_output)
})
### test function on 5 data types for new generilized function
test_that("run_comparison_5_datasets", {
set.seed(1)
tumor_exp_file <- system.file("extdata", "mock_5_data_types", "tumor_exp.txt", package="tumorcomparer")
tumor_cna_file <- system.file("extdata", "mock_5_data_types", "tumor_cna.txt", package="tumorcomparer")
tumor_meth_file <- system.file("extdata", "mock_5_data_types", "tumor_meth.txt", package="tumorcomparer")
tumor_mut_file <- system.file("extdata", "mock_5_data_types", "tumor_mut.txt", package="tumorcomparer")
tumor_prot_file <- system.file("extdata", "mock_5_data_types", "tumor_prot.txt", package="tumorcomparer")
cell_line_exp_file <- system.file("extdata", "mock_5_data_types", "cell_line_exp.txt", package="tumorcomparer")
cell_line_cna_file <- system.file("extdata", "mock_5_data_types", "cell_line_cna.txt", package="tumorcomparer")
cell_line_meth_file <- system.file("extdata", "mock_5_data_types", "cell_line_meth.txt", package="tumorcomparer")
cell_line_mut_file <- system.file("extdata", "mock_5_data_types", "cell_line_mut.txt", package="tumorcomparer")
cell_line_prot_file <- system.file("extdata", "mock_5_data_types", "cell_line_prot.txt", package="tumorcomparer")
known_cancer_gene_weights_exp_file <- system.file("extdata", "mock_5_data_types", "default_weights_for_known_cancer_genes_exp.txt", package="tumorcomparer")
known_cancer_gene_weights_cna_file <- system.file("extdata", "mock_5_data_types", "default_weights_for_known_cancer_genes_cna.txt", package="tumorcomparer")
known_cancer_gene_weights_meth_file <- system.file("extdata", "mock_5_data_types", "default_weights_for_known_cancer_genes_meth.txt", package="tumorcomparer")
known_cancer_gene_weights_mut_file <- system.file("extdata", "mock_5_data_types", "default_weights_for_known_cancer_genes_mut.txt", package="tumorcomparer")
known_cancer_gene_weights_prot_file <- system.file("extdata", "mock_5_data_types", "default_weights_for_known_cancer_genes_prot.txt", package="tumorcomparer")
cancer_specific_gene_weights_exp_file <- system.file("extdata", "mock_5_data_types", "Genes_and_weights_exp.txt", package="tumorcomparer")
cancer_specific_gene_weights_cna_file <- system.file("extdata", "mock_5_data_types", "Genes_and_weights_cna.txt", package="tumorcomparer")
cancer_specific_gene_weights_meth_file <- system.file("extdata", "mock_5_data_types", "Genes_and_weights_meth.txt", package="tumorcomparer")
cancer_specific_gene_weights_mut_file <- system.file("extdata", "mock_5_data_types", "Genes_and_weights_mut.txt", package="tumorcomparer")
cancer_specific_gene_weights_prot_file <- system.file("extdata", "mock_5_data_types", "Genes_and_weights_prot.txt", package="tumorcomparer")
### creating config list for comparison function
config_list <- list(exp=list(dataset_name = "exp", data_type_weight=1/5, default_weight = 0.01,
tumor_file = tumor_exp_file, cell_line_file = cell_line_exp_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_exp_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_exp_file),
cna=list(dataset_name = "cna", data_type_weight=1/5, default_weight = 0.01,
tumor_file = tumor_cna_file, cell_line_file = cell_line_cna_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_cna_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_cna_file),
meth=list(dataset_name = "meth", data_type_weight=1/5, default_weight = 0.01,
tumor_file = tumor_meth_file, cell_line_file = cell_line_meth_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_meth_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_meth_file),
mut=list(dataset_name = "mut", data_type_weight=1/5, default_weight = 0.01,
tumor_file = tumor_mut_file, cell_line_file = cell_line_mut_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_mut_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_mut_file),
prot=list(dataset_name = "prot", data_type_weight=1/5, default_weight = 0.01,
tumor_file = tumor_prot_file, cell_line_file = cell_line_prot_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_prot_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_prot_file)
)
test_results <- run_comparison_config_list(config_list = config_list)
#saveRDS(test_results, "inst/test_output/comparison_5_datasets_20211019.rds")
#x <- readRDS("inst/test_output/comparison_5_datasets_20211019.rds")
#expect_equal(comparison_result, x, tolerance = 0.001)
saved_output <- readRDS(system.file("test_output", "comparison_5_datasets.rds", package="tumorcomparer"))
expect_equal(test_results, saved_output)
})
### test function on 3 data types for new generilized function with specified gene_list_argument
test_that("run_comparison_config_list", {
set.seed(1)
tumor_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_mut.txt", package="tumorcomparer")
tumor_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_cna.txt", package="tumorcomparer")
tumor_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_exp.txt", package="tumorcomparer")
cell_line_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_mut.txt", package="tumorcomparer")
cell_line_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_cna.txt", package="tumorcomparer")
cell_line_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_exp.txt", package="tumorcomparer")
known_cancer_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_mut.txt", package="tumorcomparer")
known_cancer_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_cna.txt", package="tumorcomparer")
known_cancer_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_exp.txt", package="tumorcomparer")
cancer_specific_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_mut.txt", package="tumorcomparer")
cancer_specific_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_cna.txt", package="tumorcomparer")
cancer_specific_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_exp.txt", package="tumorcomparer")
sample_gene_list <- c("ARRDC1", "CNTN6", "CREBBP", "EP300", "HES1", "HES2", "HES3", "HES4", "HES5", "HEY1",
"HEY2", "HEYL", "KAT2B", "KDM5A", "NOTCH1", "NOTCH2", "NOTCH3", "NOTCH4", "NOV", "NRARP",
"PSEN2", "LFNG", "ITCH", "NCSTN", "SPEN", "JAG1", "APH1A", "FBXW7", "FHL1", "THBS2", "HDAC2",
"MFAP2", "CUL1", "RFNG", "NCOR1", "NCOR2", "MFAP5", "HDAC1", "NUMB", "JAG2", "MAML3", "MFNG",
"CIR1", "CNTN1", "MAML1", "MAML2", "NUMBL", "PSEN1", "PSENEN", "RBPJ", "RBPJL", "RBX1", "SAP30",
"SKP1", "SNW1", "CTBP1", "CTBP2", "ADAM10", "APH1B", "ADAM17", "DLK1", "DLL1", "DLL3", "DLL4", "DNER",
"DTX1", "DTX2", "DTX3", "DTX3L", "DTX4", "EGFL7", "TMEM129", "ADRA2C", "SLC2A9", "RAD54B", "MAP3K1", "EIF3E",
"WDYHV1")
### creating config list for comparison function
config_list <- list(mut=list(dataset_name = "mut", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_mut_file, cell_line_file = cell_line_mut_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_mut_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_mut_file),
cna=list(dataset_name = "cna", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_cna_file, cell_line_file = cell_line_cna_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_cna_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_cna_file),
exp=list(dataset_name = "exp", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_exp_file, cell_line_file = cell_line_exp_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_exp_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_exp_file)
)
comparison_result <- run_comparison_config_list(config_list = config_list, gene_list = sample_gene_list)
#saveRDS(comparison_result, "inst/test_output/comparison_geneset_20211019.rds")
#x <- readRDS("inst/test_output/comparison_geneset_20211019.rds")
#expect_equal(comparison_result, x, tolerance = 0.001)
saved_output <- readRDS(system.file("test_output", "comparison_geneset.rds", package="tumorcomparer"))
# print(str(comparison_result))
# print(str(saved_output))
expect_equal(comparison_result, saved_output, tolerance = 0.1)
# expect_equal(TRUE, TRUE)
})
## minimum gene number test
test_that("testing few genes error", {
set.seed(1)
tumor_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_mut.txt", package="tumorcomparer")
tumor_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_cna.txt", package="tumorcomparer")
tumor_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_exp.txt", package="tumorcomparer")
cell_line_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_mut.txt", package="tumorcomparer")
cell_line_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_cna.txt", package="tumorcomparer")
cell_line_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_exp.txt", package="tumorcomparer")
known_cancer_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_mut.txt", package="tumorcomparer")
known_cancer_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_cna.txt", package="tumorcomparer")
known_cancer_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_exp.txt", package="tumorcomparer")
cancer_specific_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_mut.txt", package="tumorcomparer")
cancer_specific_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_cna.txt", package="tumorcomparer")
cancer_specific_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_exp.txt", package="tumorcomparer")
sample_gene_list <- c("ARRDC1", "CNTN6", "CREBBP")
### creating config list for comparison function
config_list <- list(mut=list(dataset_name = "mut", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_mut_file, cell_line_file = cell_line_mut_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_mut_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_mut_file),
cna=list(dataset_name = "cna", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_cna_file, cell_line_file = cell_line_cna_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_cna_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_cna_file),
exp=list(dataset_name = "exp", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_exp_file, cell_line_file = cell_line_exp_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_exp_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_exp_file)
)
comparison_failed <- try(comparison_result <- run_comparison_config_list(config_list = config_list, gene_list = sample_gene_list), silent = TRUE)
comparison_failed <- unlist(strsplit(comparison_failed[1], split = '\n', fixed = T))[2]
test_comparison <- grepl("ERROR", comparison_failed)
expect_true(test_comparison)
})
## test for cyj_graph_maker_from_dist_mat function
test_that("cyj_graph_maker_from_dist_mat", {
set.seed(1)
tumor_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_mut.txt", package="tumorcomparer")
tumor_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_cna.txt", package="tumorcomparer")
tumor_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_exp.txt", package="tumorcomparer")
cell_line_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_mut.txt", package="tumorcomparer")
cell_line_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_cna.txt", package="tumorcomparer")
cell_line_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_exp.txt", package="tumorcomparer")
known_cancer_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_mut.txt", package="tumorcomparer")
known_cancer_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_cna.txt", package="tumorcomparer")
known_cancer_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_exp.txt", package="tumorcomparer")
cancer_specific_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_mut.txt", package="tumorcomparer")
cancer_specific_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_cna.txt", package="tumorcomparer")
cancer_specific_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_exp.txt", package="tumorcomparer")
### creating config list for comparison function
config_list <- list(mut=list(dataset_name = "mut", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_mut_file, cell_line_file = cell_line_mut_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_mut_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_mut_file),
cna=list(dataset_name = "cna", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_cna_file, cell_line_file = cell_line_cna_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_cna_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_cna_file),
exp=list(dataset_name = "exp", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_exp_file, cell_line_file = cell_line_exp_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_exp_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_exp_file)
)
comparison_result <- run_comparison_config_list(config_list = config_list)
cyj_json_graph <- cyj_graph_maker_from_dist_mat(dist_mat = comparison_result$dist_mat, min_weight = 0.85)
saved_output <- readRDS(system.file("test_output", "cyj_json_graph.rds", package="tumorcomparer"))
expect_equal(cyj_json_graph, saved_output)
})
## test for ballon_plot_data_to_result_table function
test_that("ballon_plot_data_to_result_table", {
set.seed(1)
tumor_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_mut.txt", package="tumorcomparer")
tumor_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_cna.txt", package="tumorcomparer")
tumor_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_exp.txt", package="tumorcomparer")
cell_line_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_mut.txt", package="tumorcomparer")
cell_line_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_cna.txt", package="tumorcomparer")
cell_line_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_exp.txt", package="tumorcomparer")
known_cancer_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_mut.txt", package="tumorcomparer")
known_cancer_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_cna.txt", package="tumorcomparer")
known_cancer_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_exp.txt", package="tumorcomparer")
cancer_specific_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_mut.txt", package="tumorcomparer")
cancer_specific_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_cna.txt", package="tumorcomparer")
cancer_specific_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_exp.txt", package="tumorcomparer")
### creating config list for comparison function
config_list <- list(mut=list(dataset_name = "mut", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_mut_file, cell_line_file = cell_line_mut_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_mut_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_mut_file),
cna=list(dataset_name = "cna", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_cna_file, cell_line_file = cell_line_cna_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_cna_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_cna_file),
exp=list(dataset_name = "exp", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_exp_file, cell_line_file = cell_line_exp_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_exp_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_exp_file)
)
comparison_result <- run_comparison_config_list(config_list = config_list)
plot_data <- list(plot_data = make_balloon_plot_data_from_comparison_result(comparison_result = comparison_result))
result_table <- ballon_plot_data_to_result_table(plot_data = plot_data)
saved_output <- readRDS(system.file("test_output", "baloon_plot_result_table.rds", package="tumorcomparer"))
expect_equal(result_table, saved_output)
# expect_equal(TRUE, TRUE)
})
test_that("check_zenodo_usage", {
# NOTE: GitHub Actions memory issues on Windows
skip_on_os(os = "windows")
## ----loadLibraries, message=FALSE, warning=FALSE-------------------------------------------------------------------
# Set timeout for download to 10 minutes
options(timeout=600)
data("tcga_pancan_pathway_genes")
## ------------------------------------------------------------------------------------------------------------------
# Data extracted for archive: https://zenodo.org/record/4627644/files/tc_data_pancancer_march2021.tar.gz?download=1
tc_dataset_dir <- "~/default/workspaceNotSynced/tumorcomparer_data/TC_Data_PanCancer_March2021/"
if(!dir.exists(tc_dataset_dir)) {
# Download and extract dataset
tmp_file <- tempfile(fileext=".tar.gz")
tmp_dir <- tempdir()
# NOTE: https://stackoverflow.com/questions/60985743/untar-on-windows-tar-exe-error-opening-archive-gzip-decompression-failed
download.file("https://zenodo.org/record/4627644/files/tc_data_pancancer_march2021.tar.gz?download=1", tmp_file, mode = "wb")
untar(tmp_file, exdir=tmp_dir)
tc_dataset_dir <- file.path(tmp_dir, "TC_Data_PanCancer_March2021")
}
## ------------------------------------------------------------------------------------------------------------------
gene_list <- tcga_pancan_pathway_genes[['TGF-Beta']]
cancer_type <- "LIHC"
remove_tmp_files <- FALSE
remove_errored_dataset_comparisons <- FALSE
comparison_result <- tc_geneset_comparison(
gene_list=gene_list,
cancer_type=cancer_type,
tc_dataset_dir=tc_dataset_dir,
remove_errored_dataset_comparisons=remove_errored_dataset_comparisons,
remove_tmp_files=remove_tmp_files,
verbose=TRUE)
expect_true(class(comparison_result) == "list")
## ------------------------------------------------------------------------------------------------------------------
CCLP_Expression_Quantile_Normalized <- data.table::fread(input=file.path(tc_dataset_dir, "CCLP_Expression_Quantile_Normalized.txt"))
CCLP_GISTIC_all_data_by_genes <- data.table::fread(input=file.path(tc_dataset_dir, "CCLP_GISTIC_all_data_by_genes.txt"))
mut_mat_CCLP_after_Annovar <- data.table::fread(input=file.path(tc_dataset_dir, "CCLP_mutation_matrix.txt"))
tmp_cclp_ids <- read.table(file.path(tc_dataset_dir, "CCLP_ID_and_Cancer_Type.txt"), sep="\t", header=TRUE, stringsAsFactors=FALSE)
tmp_cclp_ids <- tmp_cclp_ids$Model_name[tmp_cclp_ids$TCGA_Type == "SKCM"]
all_cclp_ids <- Reduce(intersect, list(tmp_cclp_ids,
colnames(mut_mat_CCLP_after_Annovar),
colnames(CCLP_GISTIC_all_data_by_genes),
colnames(CCLP_Expression_Quantile_Normalized)))
TCGA_Expression_Quantile_Normalized <- data.table::fread(input=file.path(tc_dataset_dir, "TCGA_Expression_Quantile_Normalized.txt"))
TCGA_GISTIC_all_data_by_genes <- data.table::fread(input=file.path(tc_dataset_dir, "TCGA_GISTIC_all_data_by_genes.txt"))
mut_mat_TCGA_after_Annovar <- data.table::fread(input=file.path(tc_dataset_dir, "TCGA_mutation_matrix.txt"))
tmp_tcga_ids <- read.table(file.path(tc_dataset_dir, "TCGA_ID_and_Cancer_Type.txt"), sep="\t", header=TRUE, stringsAsFactors=FALSE)
tmp_tcga_ids <- tmp_tcga_ids$TCGA_ID[tmp_tcga_ids$Cancer_Type == "COAD"]
all_tcga_ids <- Reduce(intersect, list(tmp_tcga_ids,
colnames(mut_mat_TCGA_after_Annovar),
colnames(TCGA_GISTIC_all_data_by_genes),
colnames(TCGA_Expression_Quantile_Normalized)))
cclp_ids <- all_cclp_ids[12:21]
tcga_ids <- all_tcga_ids[2:101]
comparison_result <- tc_geneset_comparison(
gene_list=gene_list,
cclp_ids=cclp_ids,
tcga_ids=tcga_ids,
tc_dataset_dir=tc_dataset_dir,
remove_errored_dataset_comparisons=remove_errored_dataset_comparisons,
remove_tmp_files=remove_tmp_files,
verbose=TRUE)
expect_true(class(comparison_result) == "list")
})
cannin/tumorcomparer documentation built on Feb. 7, 2023, 3:13 p.m.
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# All tests are done on files in package using system.file()
test_that("sanity_check", {
expect_equal(2 * 2, 4)
})
# TODO Add tests
# test_that("plot_mds", {
# expect_equal(TRUE, FALSE)
# })
# test_that("run_shiny_app", {
# expect_equal(TRUE, TRUE)
# })
test_that("test_tar_working", {
# Constructing the example tar.gz file
# tar cvzf inst/extdata/mock_5_data_types.tar.gz ./inst/extdata/mock_5_data_types
tmp_dir <- tempdir()
# The example file should exist
test_file <- system.file('extdata/mock_5_data_types.tar.gz', package="tumorcomparer")
expect_true(file.exists(test_file))
# The compressed file should have files inside
files <- untar(test_file, list=TRUE)
files
expect_true(length(files) > 2)
# The uncompressed file should have multiple lines in it
untar(test_file, exdir=tmp_dir)
tmp_file <- file.path(tmp_dir, files[2])
expect_true(length(readLines(tmp_file)) > 2)
})
test_that("return_first_part", {
tmp <- return_first_part("22RV1_PROSTRATE")
expect_equal(tmp, "22RV1")
})
test_that("keep_only_high_level_cnas", {
set.seed(1)
tmp <- sample(c(-2, -1, 0, 1, 2), 100, replace=TRUE)
mat <- matrix(tmp, 10, 10)
results <- as.vector(keep_only_high_level_cnas(cna_mat=mat))
expect_false(any(results == 1 | results == -1))
})
test_that("keep_only_high_level_cnas", {
t1 <- as.matrix(c(1,1,1,1,1,1,2,2,2,3,3,3,4,4))
t2 <- as.matrix(rev(t1))
weight <- c(.5,.5,.5,.5,.5,1,1,1,1,2,2,2,2,2)
results <- calc_weighted_corr(t1, t2, weight)
expect_equal(results, matrix(-0.8108894, 1, 1))
})
test_that("compute_freq_alt", {
set.seed(1)
tmp <- sample(c(0, 1), 100, replace=TRUE)
mat <- matrix(tmp, 10, 10)
expect_equal(0.51, compute_freq_alt(mat))
})
test_that("categorize_cell_lines", {
comparison_result <- readRDS(system.file("test_output", "ov_comparison_result.rds", package="tumorcomparer"))
categorization_list <- categorize_cell_lines(
num_tumors_for_comparison=length(comparison_result$tumor_ids)-1,
dist_mat=comparison_result$dist_mat,
cell_line_ids=comparison_result$cell_line_ids,
tumor_ids=comparison_result$tumor_ids,
trim_cell_line_names=FALSE)
expect_equal(categorization_list$categorization$Sample_ID[c(1,6,13)], c("OAW-28", "OV-17R", "OVK-18"))
expect_equal(categorization_list$categorization$Category[c(1,6,13)], c("Moderately Good", "Poor", "Outlier"))
})
test_that("generate_composite_mat_and_gene_weights", {
mut_default_weight <- 0.01
tumor_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_mut.txt", package="tumorcomparer")
cell_line_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_mut.txt", package="tumorcomparer")
known_cancer_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_mut.txt", package="tumorcomparer")
cancer_specific_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_mut.txt", package="tumorcomparer")
composite_mat <- generate_composite_mat_and_gene_weights(
default_weight=mut_default_weight,
tumor_file=tumor_mut_file,
cell_line_file=cell_line_mut_file,
known_cancer_gene_weights_file=known_cancer_gene_weights_mut_file,
cancer_specific_gene_weights_file=cancer_specific_gene_weights_mut_file)
#saveRDS(composite_mat, "inst/test_output/ov_composite_mat.rds")
#x <- readRDS("inst/test_output/ov_composite_mat.rds")
#expect_equal(composite_mat, x, tolerance = 0.001)
saved_output <- readRDS(system.file("test_output", "ov_composite_mat.rds", package="tumorcomparer"))
expect_equal(composite_mat, saved_output, tolerance = 0.001)
})
test_that("map_mean_similarity_to_gradient", {
comparison_result <- readRDS(system.file("test_output", "ov_comparison_result.rds", package="tumorcomparer"))
categorization_list <- categorize_cell_lines(
num_tumors_for_comparison=length(comparison_result$tumor_ids)-1,
dist_mat=comparison_result$dist_mat,
cell_line_ids=comparison_result$cell_line_ids,
tumor_ids=comparison_result$tumor_ids,
trim_cell_line_names=FALSE)
result <- map_mean_similarity_to_gradient(
mean_similarity_cell_line_to_k_nearest_tumors=categorization_list$mean_similarity_cell_line_to_k_nearest_tumors,
mean_similarity_tumor_to_k_nearest_tumors=categorization_list$mean_similarity_tumor_to_k_nearest_tumors,
col1="orange",
col2="blue",
numshades=100)
expect_equal(result[1:3], c("#DD8F21", "#F9A105", "#C37E3B"))
})
test_that("pair_dist", {
set.seed(1)
n <- 100
x <- sample(c(0, 1), n, replace=TRUE)
y <- sample(c(0, 1), n, replace=TRUE)
weights <- rnorm(n)
result <- pair_dist(x, y, weights)
expect_equal(result, 2.398, tolerance = 0.01)
})
test_that("run_comparison", {
set.seed(1)
tumor_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_mut.txt", package="tumorcomparer")
tumor_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_cna.txt", package="tumorcomparer")
tumor_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_exp.txt", package="tumorcomparer")
cell_line_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_mut.txt", package="tumorcomparer")
cell_line_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_cna.txt", package="tumorcomparer")
cell_line_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_exp.txt", package="tumorcomparer")
known_cancer_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_mut.txt", package="tumorcomparer")
known_cancer_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_cna.txt", package="tumorcomparer")
known_cancer_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_exp.txt", package="tumorcomparer")
cancer_specific_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_mut.txt", package="tumorcomparer")
cancer_specific_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_cna.txt", package="tumorcomparer")
cancer_specific_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_exp.txt", package="tumorcomparer")
comparison_result <- run_comparison(
available_data_types=c("mut", "cna", "exp"),
mut_data_type_weight = 1/3,
cna_data_type_weight = 1/3,
exp_data_type_weight = 1/3,
cna_default_weight=0.01,
mut_default_weight=0.01,
exp_default_weight=0.01,
tumor_mut_file=tumor_mut_file,
tumor_cna_file=tumor_cna_file,
tumor_exp_file=tumor_exp_file,
cell_line_mut_file=cell_line_mut_file,
cell_line_cna_file=cell_line_cna_file,
cell_line_exp_file=cell_line_exp_file,
known_cancer_gene_weights_mut_file=known_cancer_gene_weights_mut_file,
known_cancer_gene_weights_cna_file=known_cancer_gene_weights_cna_file,
known_cancer_gene_weights_exp_file=known_cancer_gene_weights_exp_file,
cancer_specific_gene_weights_mut_file=cancer_specific_gene_weights_mut_file,
cancer_specific_gene_weights_cna_file=cancer_specific_gene_weights_cna_file,
cancer_specific_gene_weights_exp_file=cancer_specific_gene_weights_exp_file)
#saveRDS(comparison_result, "inst/test_output/ov_comparison_result.rds")
#x <- readRDS("inst/test_output/ov_comparison_result.rds")
#expect_equal(comparison_result, x, tolerance = 0.001)
saved_output <- readRDS(system.file("test_output", "ov_comparison_result.rds", package="tumorcomparer"))
expect_equal(comparison_result, saved_output)
})
### test function on 3 data types for new generilized function
test_that("run_comparison_config_list", {
set.seed(1)
tumor_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_mut.txt", package="tumorcomparer")
tumor_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_cna.txt", package="tumorcomparer")
tumor_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_exp.txt", package="tumorcomparer")
cell_line_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_mut.txt", package="tumorcomparer")
cell_line_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_cna.txt", package="tumorcomparer")
cell_line_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_exp.txt", package="tumorcomparer")
known_cancer_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_mut.txt", package="tumorcomparer")
known_cancer_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_cna.txt", package="tumorcomparer")
known_cancer_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_exp.txt", package="tumorcomparer")
cancer_specific_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_mut.txt", package="tumorcomparer")
cancer_specific_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_cna.txt", package="tumorcomparer")
cancer_specific_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_exp.txt", package="tumorcomparer")
### creating config list for comparison function
config_list <- list(mut=list(dataset_name = "mut", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_mut_file, cell_line_file = cell_line_mut_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_mut_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_mut_file),
cna=list(dataset_name = "cna", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_cna_file, cell_line_file = cell_line_cna_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_cna_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_cna_file),
exp=list(dataset_name = "exp", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_exp_file, cell_line_file = cell_line_exp_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_exp_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_exp_file)
)
comparison_result <- run_comparison_config_list(config_list = config_list)
#saveRDS(comparison_result, "inst/test_output/comparison_config.rds")
#x <- readRDS("inst/test_output/comparison_config.rds")
#expect_equal(comparison_result, x, tolerance = 0.001)
saved_output <- readRDS(system.file("test_output", "comparison_config.rds", package="tumorcomparer"))
expect_equal(comparison_result, saved_output)
})
test_that("run_comparison_two_datasets", {
set.seed(1)
tumor_mut_file <- system.file("extdata", "READ_data_for_running_TC", "tumor_mut.txt", package="tumorcomparer")
tumor_exp_file <- system.file("extdata", "READ_data_for_running_TC", "tumor_exp.txt", package="tumorcomparer")
cell_line_mut_file <- system.file("extdata", "READ_data_for_running_TC", "cell_line_mut.txt", package="tumorcomparer")
cell_line_exp_file <- system.file("extdata", "READ_data_for_running_TC", "cell_line_exp.txt", package="tumorcomparer")
known_cancer_gene_weights_mut_file <- system.file("extdata", "READ_data_for_running_TC", "default_weights_for_known_cancer_genes_mut.txt", package="tumorcomparer")
known_cancer_gene_weights_exp_file <- system.file("extdata", "READ_data_for_running_TC", "default_weights_for_known_cancer_genes_exp.txt", package="tumorcomparer")
cancer_specific_gene_weights_mut_file <- system.file("extdata", "READ_data_for_running_TC", "Genes_and_weights_mut.txt", package="tumorcomparer")
cancer_specific_gene_weights_exp_file <- system.file("extdata", "READ_data_for_running_TC", "Genes_and_weights_exp.txt", package="tumorcomparer")
comparison_result <- run_comparison(
available_data_types=c("mut", "exp"),
mut_data_type_weight = 1/2,
exp_data_type_weight = 1/2,
cna_default_weight=0.01,
exp_default_weight=0.01,
tumor_mut_file=tumor_mut_file,
tumor_exp_file=tumor_exp_file,
cell_line_mut_file=cell_line_mut_file,
cell_line_exp_file=cell_line_exp_file,
known_cancer_gene_weights_mut_file=known_cancer_gene_weights_mut_file,
known_cancer_gene_weights_exp_file=known_cancer_gene_weights_exp_file,
cancer_specific_gene_weights_mut_file=cancer_specific_gene_weights_mut_file,
cancer_specific_gene_weights_exp_file=cancer_specific_gene_weights_exp_file)
#saveRDS(comparison_result, "inst/test_output/comparison_2_datasets.rds")
#x <- readRDS("inst/test_output/comparison_2_datasets.rds")
#expect_equal(comparison_result, x, tolerance = 0.001)
saved_output <- readRDS(system.file("test_output", "comparison_2_datasets.rds", package="tumorcomparer"))
expect_equal(comparison_result, saved_output)
})
### test function on 5 data types for new generilized function
test_that("run_comparison_5_datasets", {
set.seed(1)
tumor_exp_file <- system.file("extdata", "mock_5_data_types", "tumor_exp.txt", package="tumorcomparer")
tumor_cna_file <- system.file("extdata", "mock_5_data_types", "tumor_cna.txt", package="tumorcomparer")
tumor_meth_file <- system.file("extdata", "mock_5_data_types", "tumor_meth.txt", package="tumorcomparer")
tumor_mut_file <- system.file("extdata", "mock_5_data_types", "tumor_mut.txt", package="tumorcomparer")
tumor_prot_file <- system.file("extdata", "mock_5_data_types", "tumor_prot.txt", package="tumorcomparer")
cell_line_exp_file <- system.file("extdata", "mock_5_data_types", "cell_line_exp.txt", package="tumorcomparer")
cell_line_cna_file <- system.file("extdata", "mock_5_data_types", "cell_line_cna.txt", package="tumorcomparer")
cell_line_meth_file <- system.file("extdata", "mock_5_data_types", "cell_line_meth.txt", package="tumorcomparer")
cell_line_mut_file <- system.file("extdata", "mock_5_data_types", "cell_line_mut.txt", package="tumorcomparer")
cell_line_prot_file <- system.file("extdata", "mock_5_data_types", "cell_line_prot.txt", package="tumorcomparer")
known_cancer_gene_weights_exp_file <- system.file("extdata", "mock_5_data_types", "default_weights_for_known_cancer_genes_exp.txt", package="tumorcomparer")
known_cancer_gene_weights_cna_file <- system.file("extdata", "mock_5_data_types", "default_weights_for_known_cancer_genes_cna.txt", package="tumorcomparer")
known_cancer_gene_weights_meth_file <- system.file("extdata", "mock_5_data_types", "default_weights_for_known_cancer_genes_meth.txt", package="tumorcomparer")
known_cancer_gene_weights_mut_file <- system.file("extdata", "mock_5_data_types", "default_weights_for_known_cancer_genes_mut.txt", package="tumorcomparer")
known_cancer_gene_weights_prot_file <- system.file("extdata", "mock_5_data_types", "default_weights_for_known_cancer_genes_prot.txt", package="tumorcomparer")
cancer_specific_gene_weights_exp_file <- system.file("extdata", "mock_5_data_types", "Genes_and_weights_exp.txt", package="tumorcomparer")
cancer_specific_gene_weights_cna_file <- system.file("extdata", "mock_5_data_types", "Genes_and_weights_cna.txt", package="tumorcomparer")
cancer_specific_gene_weights_meth_file <- system.file("extdata", "mock_5_data_types", "Genes_and_weights_meth.txt", package="tumorcomparer")
cancer_specific_gene_weights_mut_file <- system.file("extdata", "mock_5_data_types", "Genes_and_weights_mut.txt", package="tumorcomparer")
cancer_specific_gene_weights_prot_file <- system.file("extdata", "mock_5_data_types", "Genes_and_weights_prot.txt", package="tumorcomparer")
### creating config list for comparison function
config_list <- list(exp=list(dataset_name = "exp", data_type_weight=1/5, default_weight = 0.01,
tumor_file = tumor_exp_file, cell_line_file = cell_line_exp_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_exp_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_exp_file),
cna=list(dataset_name = "cna", data_type_weight=1/5, default_weight = 0.01,
tumor_file = tumor_cna_file, cell_line_file = cell_line_cna_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_cna_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_cna_file),
meth=list(dataset_name = "meth", data_type_weight=1/5, default_weight = 0.01,
tumor_file = tumor_meth_file, cell_line_file = cell_line_meth_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_meth_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_meth_file),
mut=list(dataset_name = "mut", data_type_weight=1/5, default_weight = 0.01,
tumor_file = tumor_mut_file, cell_line_file = cell_line_mut_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_mut_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_mut_file),
prot=list(dataset_name = "prot", data_type_weight=1/5, default_weight = 0.01,
tumor_file = tumor_prot_file, cell_line_file = cell_line_prot_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_prot_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_prot_file)
)
test_results <- run_comparison_config_list(config_list = config_list)
#saveRDS(test_results, "inst/test_output/comparison_5_datasets_20211019.rds")
#x <- readRDS("inst/test_output/comparison_5_datasets_20211019.rds")
#expect_equal(comparison_result, x, tolerance = 0.001)
saved_output <- readRDS(system.file("test_output", "comparison_5_datasets.rds", package="tumorcomparer"))
expect_equal(test_results, saved_output)
})
### test function on 3 data types for new generilized function with specified gene_list_argument
test_that("run_comparison_config_list", {
set.seed(1)
tumor_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_mut.txt", package="tumorcomparer")
tumor_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_cna.txt", package="tumorcomparer")
tumor_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_exp.txt", package="tumorcomparer")
cell_line_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_mut.txt", package="tumorcomparer")
cell_line_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_cna.txt", package="tumorcomparer")
cell_line_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_exp.txt", package="tumorcomparer")
known_cancer_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_mut.txt", package="tumorcomparer")
known_cancer_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_cna.txt", package="tumorcomparer")
known_cancer_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_exp.txt", package="tumorcomparer")
cancer_specific_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_mut.txt", package="tumorcomparer")
cancer_specific_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_cna.txt", package="tumorcomparer")
cancer_specific_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_exp.txt", package="tumorcomparer")
sample_gene_list <- c("ARRDC1", "CNTN6", "CREBBP", "EP300", "HES1", "HES2", "HES3", "HES4", "HES5", "HEY1",
"HEY2", "HEYL", "KAT2B", "KDM5A", "NOTCH1", "NOTCH2", "NOTCH3", "NOTCH4", "NOV", "NRARP",
"PSEN2", "LFNG", "ITCH", "NCSTN", "SPEN", "JAG1", "APH1A", "FBXW7", "FHL1", "THBS2", "HDAC2",
"MFAP2", "CUL1", "RFNG", "NCOR1", "NCOR2", "MFAP5", "HDAC1", "NUMB", "JAG2", "MAML3", "MFNG",
"CIR1", "CNTN1", "MAML1", "MAML2", "NUMBL", "PSEN1", "PSENEN", "RBPJ", "RBPJL", "RBX1", "SAP30",
"SKP1", "SNW1", "CTBP1", "CTBP2", "ADAM10", "APH1B", "ADAM17", "DLK1", "DLL1", "DLL3", "DLL4", "DNER",
"DTX1", "DTX2", "DTX3", "DTX3L", "DTX4", "EGFL7", "TMEM129", "ADRA2C", "SLC2A9", "RAD54B", "MAP3K1", "EIF3E",
"WDYHV1")
### creating config list for comparison function
config_list <- list(mut=list(dataset_name = "mut", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_mut_file, cell_line_file = cell_line_mut_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_mut_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_mut_file),
cna=list(dataset_name = "cna", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_cna_file, cell_line_file = cell_line_cna_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_cna_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_cna_file),
exp=list(dataset_name = "exp", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_exp_file, cell_line_file = cell_line_exp_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_exp_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_exp_file)
)
comparison_result <- run_comparison_config_list(config_list = config_list, gene_list = sample_gene_list)
#saveRDS(comparison_result, "inst/test_output/comparison_geneset_20211019.rds")
#x <- readRDS("inst/test_output/comparison_geneset_20211019.rds")
#expect_equal(comparison_result, x, tolerance = 0.001)
saved_output <- readRDS(system.file("test_output", "comparison_geneset.rds", package="tumorcomparer"))
# print(str(comparison_result))
# print(str(saved_output))
expect_equal(comparison_result, saved_output, tolerance = 0.1)
# expect_equal(TRUE, TRUE)
})
## minimum gene number test
test_that("testing few genes error", {
set.seed(1)
tumor_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_mut.txt", package="tumorcomparer")
tumor_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_cna.txt", package="tumorcomparer")
tumor_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_exp.txt", package="tumorcomparer")
cell_line_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_mut.txt", package="tumorcomparer")
cell_line_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_cna.txt", package="tumorcomparer")
cell_line_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_exp.txt", package="tumorcomparer")
known_cancer_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_mut.txt", package="tumorcomparer")
known_cancer_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_cna.txt", package="tumorcomparer")
known_cancer_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_exp.txt", package="tumorcomparer")
cancer_specific_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_mut.txt", package="tumorcomparer")
cancer_specific_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_cna.txt", package="tumorcomparer")
cancer_specific_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_exp.txt", package="tumorcomparer")
sample_gene_list <- c("ARRDC1", "CNTN6", "CREBBP")
### creating config list for comparison function
config_list <- list(mut=list(dataset_name = "mut", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_mut_file, cell_line_file = cell_line_mut_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_mut_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_mut_file),
cna=list(dataset_name = "cna", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_cna_file, cell_line_file = cell_line_cna_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_cna_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_cna_file),
exp=list(dataset_name = "exp", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_exp_file, cell_line_file = cell_line_exp_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_exp_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_exp_file)
)
comparison_failed <- try(comparison_result <- run_comparison_config_list(config_list = config_list, gene_list = sample_gene_list), silent = TRUE)
comparison_failed <- unlist(strsplit(comparison_failed[1], split = '\n', fixed = T))[2]
test_comparison <- grepl("ERROR", comparison_failed)
expect_true(test_comparison)
})
## test for cyj_graph_maker_from_dist_mat function
test_that("cyj_graph_maker_from_dist_mat", {
set.seed(1)
tumor_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_mut.txt", package="tumorcomparer")
tumor_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_cna.txt", package="tumorcomparer")
tumor_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_exp.txt", package="tumorcomparer")
cell_line_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_mut.txt", package="tumorcomparer")
cell_line_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_cna.txt", package="tumorcomparer")
cell_line_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_exp.txt", package="tumorcomparer")
known_cancer_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_mut.txt", package="tumorcomparer")
known_cancer_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_cna.txt", package="tumorcomparer")
known_cancer_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_exp.txt", package="tumorcomparer")
cancer_specific_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_mut.txt", package="tumorcomparer")
cancer_specific_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_cna.txt", package="tumorcomparer")
cancer_specific_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_exp.txt", package="tumorcomparer")
### creating config list for comparison function
config_list <- list(mut=list(dataset_name = "mut", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_mut_file, cell_line_file = cell_line_mut_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_mut_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_mut_file),
cna=list(dataset_name = "cna", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_cna_file, cell_line_file = cell_line_cna_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_cna_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_cna_file),
exp=list(dataset_name = "exp", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_exp_file, cell_line_file = cell_line_exp_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_exp_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_exp_file)
)
comparison_result <- run_comparison_config_list(config_list = config_list)
cyj_json_graph <- cyj_graph_maker_from_dist_mat(dist_mat = comparison_result$dist_mat, min_weight = 0.85)
saved_output <- readRDS(system.file("test_output", "cyj_json_graph.rds", package="tumorcomparer"))
expect_equal(cyj_json_graph, saved_output)
})
## test for ballon_plot_data_to_result_table function
test_that("ballon_plot_data_to_result_table", {
set.seed(1)
tumor_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_mut.txt", package="tumorcomparer")
tumor_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_cna.txt", package="tumorcomparer")
tumor_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "tumor_exp.txt", package="tumorcomparer")
cell_line_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_mut.txt", package="tumorcomparer")
cell_line_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_cna.txt", package="tumorcomparer")
cell_line_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "cell_line_exp.txt", package="tumorcomparer")
known_cancer_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_mut.txt", package="tumorcomparer")
known_cancer_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_cna.txt", package="tumorcomparer")
known_cancer_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "default_weights_for_known_cancer_genes_exp.txt", package="tumorcomparer")
cancer_specific_gene_weights_mut_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_mut.txt", package="tumorcomparer")
cancer_specific_gene_weights_cna_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_cna.txt", package="tumorcomparer")
cancer_specific_gene_weights_exp_file <- system.file("extdata", "ovarian_tcga_cclp", "Genes_and_weights_exp.txt", package="tumorcomparer")
### creating config list for comparison function
config_list <- list(mut=list(dataset_name = "mut", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_mut_file, cell_line_file = cell_line_mut_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_mut_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_mut_file),
cna=list(dataset_name = "cna", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_cna_file, cell_line_file = cell_line_cna_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_cna_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_cna_file),
exp=list(dataset_name = "exp", data_type_weight=1/3, default_weight = 0.01,
tumor_file = tumor_exp_file, cell_line_file = cell_line_exp_file,
known_cancer_gene_weights_file = known_cancer_gene_weights_exp_file,
cancer_specific_gene_weights_file = cancer_specific_gene_weights_exp_file)
)
comparison_result <- run_comparison_config_list(config_list = config_list)
plot_data <- list(plot_data = make_balloon_plot_data_from_comparison_result(comparison_result = comparison_result))
result_table <- ballon_plot_data_to_result_table(plot_data = plot_data)
saved_output <- readRDS(system.file("test_output", "baloon_plot_result_table.rds", package="tumorcomparer"))
expect_equal(result_table, saved_output)
# expect_equal(TRUE, TRUE)
})
test_that("check_zenodo_usage", {
# NOTE: GitHub Actions memory issues on Windows
skip_on_os(os = "windows")
## ----loadLibraries, message=FALSE, warning=FALSE-------------------------------------------------------------------
# Set timeout for download to 10 minutes
options(timeout=600)
data("tcga_pancan_pathway_genes")
## ------------------------------------------------------------------------------------------------------------------
# Data extracted for archive: https://zenodo.org/record/4627644/files/tc_data_pancancer_march2021.tar.gz?download=1
tc_dataset_dir <- "~/default/workspaceNotSynced/tumorcomparer_data/TC_Data_PanCancer_March2021/"
if(!dir.exists(tc_dataset_dir)) {
# Download and extract dataset
tmp_file <- tempfile(fileext=".tar.gz")
tmp_dir <- tempdir()
# NOTE: https://stackoverflow.com/questions/60985743/untar-on-windows-tar-exe-error-opening-archive-gzip-decompression-failed
download.file("https://zenodo.org/record/4627644/files/tc_data_pancancer_march2021.tar.gz?download=1", tmp_file, mode = "wb")
untar(tmp_file, exdir=tmp_dir)
tc_dataset_dir <- file.path(tmp_dir, "TC_Data_PanCancer_March2021")
}
## ------------------------------------------------------------------------------------------------------------------
gene_list <- tcga_pancan_pathway_genes[['TGF-Beta']]
cancer_type <- "LIHC"
remove_tmp_files <- FALSE
remove_errored_dataset_comparisons <- FALSE
comparison_result <- tc_geneset_comparison(
gene_list=gene_list,
cancer_type=cancer_type,
tc_dataset_dir=tc_dataset_dir,
remove_errored_dataset_comparisons=remove_errored_dataset_comparisons,
remove_tmp_files=remove_tmp_files,
verbose=TRUE)
expect_true(class(comparison_result) == "list")
## ------------------------------------------------------------------------------------------------------------------
CCLP_Expression_Quantile_Normalized <- data.table::fread(input=file.path(tc_dataset_dir, "CCLP_Expression_Quantile_Normalized.txt"))
CCLP_GISTIC_all_data_by_genes <- data.table::fread(input=file.path(tc_dataset_dir, "CCLP_GISTIC_all_data_by_genes.txt"))
mut_mat_CCLP_after_Annovar <- data.table::fread(input=file.path(tc_dataset_dir, "CCLP_mutation_matrix.txt"))
tmp_cclp_ids <- read.table(file.path(tc_dataset_dir, "CCLP_ID_and_Cancer_Type.txt"), sep="\t", header=TRUE, stringsAsFactors=FALSE)
tmp_cclp_ids <- tmp_cclp_ids$Model_name[tmp_cclp_ids$TCGA_Type == "SKCM"]
all_cclp_ids <- Reduce(intersect, list(tmp_cclp_ids,
colnames(mut_mat_CCLP_after_Annovar),
colnames(CCLP_GISTIC_all_data_by_genes),
colnames(CCLP_Expression_Quantile_Normalized)))
TCGA_Expression_Quantile_Normalized <- data.table::fread(input=file.path(tc_dataset_dir, "TCGA_Expression_Quantile_Normalized.txt"))
TCGA_GISTIC_all_data_by_genes <- data.table::fread(input=file.path(tc_dataset_dir, "TCGA_GISTIC_all_data_by_genes.txt"))
mut_mat_TCGA_after_Annovar <- data.table::fread(input=file.path(tc_dataset_dir, "TCGA_mutation_matrix.txt"))
tmp_tcga_ids <- read.table(file.path(tc_dataset_dir, "TCGA_ID_and_Cancer_Type.txt"), sep="\t", header=TRUE, stringsAsFactors=FALSE)
tmp_tcga_ids <- tmp_tcga_ids$TCGA_ID[tmp_tcga_ids$Cancer_Type == "COAD"]
all_tcga_ids <- Reduce(intersect, list(tmp_tcga_ids,
colnames(mut_mat_TCGA_after_Annovar),
colnames(TCGA_GISTIC_all_data_by_genes),
colnames(TCGA_Expression_Quantile_Normalized)))
cclp_ids <- all_cclp_ids[12:21]
tcga_ids <- all_tcga_ids[2:101]
comparison_result <- tc_geneset_comparison(
gene_list=gene_list,
cclp_ids=cclp_ids,
tcga_ids=tcga_ids,
tc_dataset_dir=tc_dataset_dir,
remove_errored_dataset_comparisons=remove_errored_dataset_comparisons,
remove_tmp_files=remove_tmp_files,
verbose=TRUE)
expect_true(class(comparison_result) == "list")
})
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